Citation strategy in desert landscape

Edward

Regarding publication, shall I cite as few papers as is necessary for evidence and support, or shall I cite as many as possible to establish undeniable citation links for eternity, however unworthy is my work or their works? One is certainly tempted to adopt the latter option, which probably has a part to do with the proliferation and the lengthening of papers cited and fueled continuous in vacuous circles, and demise of trees as the age of reason grows into the age of scientocracy. It seems that an average scientific paper from 50 years ago contains many fewer references than that of today – how much of the current euphoria of citation is really attributed to scientific growth and increased complexity?

One of the most significant biology paper to have come out in the past century was George Price’s 1970 article titled Selection and Covariance. It spans three text columns in Nature and contains no reference – a solitary, immovable monument in the annals of science. It has been cited over 500 times to date.

That was a rather recent example, and a freakish one to be sure. It seems that us ordinary mortals are resigned to building self-sustaining social networks in which we cite ourselves and each others, almost by acknowledged consensus. The professional pressure to publish is so great and so reasonable, it seems unlikely that Price’s publication strategy would prevail very often. For the rest of us, is there nothing new to say?

Of course we all have something to say, even useful things, but in the back of my mind I always ruminate a more romantic version of a scientist wandering alone in vast intellectual deserts punctuated with cacti of wisdom where, at last, heroes gather, only to disperse again according to some evolutionarily stable strategy.

Biodiversity Trauma

My last week was largely structured around another bruising round with illness, lots of time in bed, plenty of spatial ecology readings, and inordinate amounts of ginger tea. With all this time to sit an think one might imagine that I emerged with some interesting thoughts on the role of space in ecological dynamics, but after two days of papers on dispersal induced population desynchronization, quasicyclic population dynamics, and spatial moment equations I felt decidedly uninspired.


Was the fault mine (i.e. do I have endogenous disinterest (little spatial ecology joke there)), or could my lack of inspiration be the result of the material too? Am I simply indifferent to ecological concepts like biodiversity, or is our approach to science is so abstract that one can hardly see the forest for the experimental trees? Are two-species reaction-diffusion models realistic portrayals of ecologic systems, and does their potential for spontaneous pattern formation help explain the origins of patchiness in the real world? How could go about addressing these questions?


I have also been reading a bit of Gilles Deluze’s Cinema 1: The Movement Image, and his commentary on Bergson’s thesis of “the whole.” Briefly, the “whole” is defined by relations, and is an indivisible continuity (i.e. it has no parts as subdivision would inevitably change it). How could this concept of the ‘whole’ relate to the scientific method, and in particular to ecology which is characterized by a phenomenal amount of relations? Are ecologic systems are in themselves ‘wholes’ in that they are defined by relations between components that work together to create the realities we perceive? And in such a case is it possible to exert a scientific focus without removing ourselves from the study of this ecologic ‘whole?’


Any theoretical ecologist will (justly) tell you that models are always approximations of reality, and that to be able to deal with analysis at all we have to keep things simple, and address the relevant questions. The same comment could, of course, be made about experimentation: in doing an experiment we remove as many extraneous interactions as possible so that we can better address the questions that we’re interested in. All of this to show that in some realities, at least, the phenomena of interest are possible, but what of our reality, the world outside that we are ostensibly interested in?


It is along these lines that I’ve been playing with the concept of a film exploring how the science of ecology is removed (alienated even) from the world it attempts to describe. The pictures here are the first stills I pulled off of some footage shot toward this aim.


Of course, my general complaint is not new, nor restricted to the sciences. In order to study anything we necessarily restrict our focus, and tend add context retrospectively: considering how other processes interact with our focal process, or adding a historical (marxist, feminist, queer, etc.) perspective to our analysis. I’m not super sure what the goal of the academy is, but let us for now assume it is to create an understanding, a narrative of consensus, that we can use to interact with the world. Certainly science has something to contribute to this understanding, but there is also a need for other epistemologies to contribute towards our understanding of ecologic concepts (and indeed other epistemologies have contributed). I suspect my bout of illness will have been the beginning of a long inquiry into just how all of our epistemologies might fit together.

The Cat's Away

With our fearless leader away in South Africa at Diversitas, followed by safari and some home time, the little Gonzalez lab mice have the run of the lab for three weeks. What sort-of rogue biodiversity science are we up to?
Here’s a list of a few things I’ve been working on, or thinking about working on.

I’m thinking about writing a review manuscript on how ecologists just flip-flop between niche and neutral ideas and never actually make much progress because no one wants to cite anything more than ten years old - A love story.

I have a suite of samples collected this summer that I’m playing with, and getting some surprisingly good data from. Depending on how the final data turn out, Jon and I will be collaborating to write a manuscript from these samples in the next few months. Should be exciting.

I’m thinking of writing a popular-style book on temperate rainforest mites. Wouldn’t your friends and family be impressed to find that on your coffee table? Lots of pictures and loaded with interesting facts. Low, low price of $19.99…maybe I’ll hold off until I find a publisher.

And, lastly, something that Michael and I have been working on (struggling with) for some time now, is a plot for our biodiversity movie. I want it to be funny, but Michael is pushing for a more serious tone. Unfortunately the rest of the lab has been reluctant to get involved (maybe they saw our last movie?) What do you think about a remake of ‘Casablanca’ using a cast of mites and collembola?

Feedback, collaborations and new ideas are always welcome.

Journal of non-significant results

Following the recent controversy surrounding publishing policies at PNAS, I got into a discussion with members of the Abouheif lab about the many quirks of scientific publishing, and some of the problems they cause for science in general, in particular:

• Loss of confidence in scientific integrity
• Publication biases

I'll focus on the second issue, which is perhaps a bit more subtle and more relevant to all scientists without getting too far into the sociology of science.
Publication bias is a concern for anyone who's ever written a review paper, conducted a meta-analysis, or interested in complex problems that require multiple experiments to tease apart interactive effects. In a nutshell, the reality is that journals aren't interested in publishing studies about non-significant results. If your study or experiment found no significant difference between treatments of interest, that's less likely to get attention (and thus improve the journal's impact factor), than statistically significant results. You can see how this can skew our perceptions of phenomena, if the only observations we are exposed to are the "interesting" ones.
Given how much we know about publication bias and the problems it causes, it has occured to Zoë and myself that what is really needed is a forum to publish all these non-significant results that no 'respectable' journal would sully their pages with. Given how easy it is to find even 'obscure' results via article databases, impact and significance may be more relevant at the scale of an individual article, rather than an entire journal (" the times, they are a-changin' ").

So, Zoë and I want to start 'the journal of non-significant results' to publish and provide access to all those results of experiments, studies, and methods that just didn't work out, or at least gave statistically non-significant, but perhaps scientifically interesting, results. Unless PLoS beats us to it (which would probably work better, actually).
Think about it for a moment:
How many grad students and research assistants have tried the same doomed method, without knowing that several people have already tried it before? How much better would results of meta-analyses become now that all the non-significant results could be included?
This is not intended to be entirely tongue-in-cheek (unlike the 'journal of irreproducible results' - that's totally different). Although it sounds cheeky, may not ever achieve the impact factor of Nature or even Ecology Letters, it would still provide a valuable and novel function in scientific publishing, with no shortage of suitable material. I think it's time to make science a little less sexy and a whole lot more practical and accurate.
In fact, this idea is not without precedent: there is already a Journal of Non-Significan Results in Education. Once again, education scientists are ahead of the curve (though apparently lagging in follow-through as the journal has yet to post it's first issue).

We also thought of the first spin-off sister journal: 'the journal of insignificant results' for results that are statistically significant, but biologically uninteresting.

Scientific revival tent

September, September, September. No month signals scholastic pursuits quite as much as the month that typically sees students of all ages returning to classes. Granted, there is really no such thing as summer vacation in biodiversity research, but September does generally mean an end to conference season, an end to field season, and the revival of campus life.

Nowhere is this revival more evident than the Gonzalez lab. After long months of separation, all of the lab members again find themselves under the same roof, and with no lack of things to do. Samples have to be processed and diagrams have to be drawn, but there are also social aspects to the return of lab-mates. Some of the lab-bonding highlights for the Gonzalez lab this fall include the following:

Lab-logo contest:

Lab members should endeavour to make a logo for the Gonzalez lab! Deadline Oct. 1, with a potential prize for the winning submission!

Biodiversity film contest:

This fall the auteurs of the Gonzalez lab have a hefty challenge on their plates, with an award for the best short made in the lab on biodiversity. Submission deadline is December 1.

Everybody put on your creative-science hats and have at it!

Working Vacation

It’s been a great month for me, here on the westcoast. I’ve been visiting friends, family, cat, car, etc. on Vancouver Island, and doing some canopy sampling while I’m here also. The project, called ABASS (Arboreal Biodiversity Across Spatial Scales), was initiated at the end of my PhD, and this year I went into the field to collect HoBo dataloggers and a few arboreal moss samples. So, it’s a working vacation of sorts. But it’s the kind of work that I love to do. Firstly, the field sites are some of the most spectacular in the world. And secondly, because it’s an area that I have a connection to, as a scientist, and also because it’s home and I have history here.

This year I visited three sites in Clayoquot Sound UNESCO Biosphere Reserve on the west coast of Vancouver Island, just north of Tofino, BC. This is ancient temperate rainforest, and canopy samples are collected from 60m Sitka Spruce trees of coastal estuaries.

Of the three sites (Sydney, Watta, Moyeha), the Sydney is my favourite; mostly for it’s pristine forests, amazing wildlife, and sheer isolation. It’s located 1.5 hours by boat from Tofino, and about 45 minutes north of the village of Ahousat, where the new national chief of the Assembly of First Nations was celebrated just last week. In the Sydney it’s just water, rock, trees and sky as far as you can see.

A typical day in the field started with collecting Blue and Huckleberries from around the camp site before canoeing off to the estuary. This year has been phenomenal for berries all over Vancouver Island, and the Huckleberries were the biggest I’ve ever seen. I work with a professional tree climber (Kev the arbornaut), who has climbed over an estimated 15,000 trees in his career (he stopped counting at 10,000). Our task is to climb 12 Sitka Spruce trees in each of the three watersheds, and collect dataloggers and moss samples for extraction of microarthropods (mainly mites). Climbing big trees, it always amazes me that they are just plants, related to a piece of celery or an African violet, and here I am clumsily climbing up them like an ant crawling up a blade of grass. At the top you can feel them sway in the wind.

Of course, also on a typical day in the field, you need to accept the good with the bad. Good parts were napping and swimming in the estuary, and watching a Humpback whale lunge feed for pilchards in the inlet for 4 hours, while we sat on the rocks, drinking beer and eating oysters. The bad parts were falling down and bashing my knee on the rocks in the dry riverbed, getting stung by a bee and having my whole arm swell-up to the point where I couldn’t bend my fingers, and stabbing myself with my pocket knife.

But, it’s almost time to wrap-up and return to Montreal. I’m anxious to get back into the lab and start some new experiments, play with moss, and see some new mites. We have at least one new addition to our lab starting sometime this fall, so it should be an exciting time in the Gonzalez lab as some people finish up their projects and new ones get underway.

I hope everyone had a great summer, and I’ll see you all soon.

Farewell to Albuquerque

Well, ESA isn't over, but the Gonzalez lab contingent is pulling out this morning, leaving the Friday sessions to hardier folks than we. And while the conference certainly felt like it was winding down tonight, ESA definitely went out with a bang.

Overall the last two days offered fantastic talks, with a particular emphasis on competition (especially among plants). Whole sessions were devoted to long-term data sets like the censused plots of Barro Colorado Island and more experimental set ups like Cedar Creek. While I definitely agree that there is much that can be learned from long-term study sites like BCI and Cedar Creek (indeed, much research would be impossible without them), I wonder as to whether there might also be a problematic side to such awesome resources as these. For example, I went to countless talks over the last two days about tropical forest dynamics, probably 90% of which were conducted on BCI. Now, it's not that BCI isn't an appropriate place to study, it's just that it seems to be the only place that is studied, which may lead us to accept idiosyncratic patterns of BCI as typical universal tropical forest trends. Similarly, it seems that so much of our knowledge on the effects of diversity on ecosystem functioning (representing another big chunk of talks I saw over the last two days) comes from Cedar Creek; and while it is an awesome study site, it seems dangerous to let just one experiment inform us so completely on a topic that is so important.

All that being said, it was one of the talks on BCI that caught my eye today, given by none other than Stephen P. Hubbell, who was at once lucid, clear, concise, and humorous. His talk also had me thinking about the nature of star power in science - as the lecture theatre was packed to the brim. People even took pictures of him. It was off the hook.

And on that note, a farewell to Albuquerque.

Dispatch from Albuqerque

The 94th annual Ecological Society of America meeting kicked off this Sunday with two, count them, two Gonzalez lab members in attendance. The theme for this year's meeting is "Ecological Knowledge and a Global Sustainable Society," and while there is some deal of murmuring that the theme is particularly ironic for a relatively isolated location that happens to be in a desert, the unique setting has inspired some interesting conversations on water issues and other elements of sustainability.

External to the meeting theme there have been some genuinely interesting talks in the desperately over-air-conditioned Albuquerque convention center. In particular over the last two days I have enjoyed an interesting special session calling for the emergence of a fully formed discipline of "warfare ecology" to address the unique and prevalent ecological challenges presented by war, and a symposium looking at interactions of ecological and evolutionary dynamics. Indeed, there have been a few shards of inspiration capable of piercing even my bitter and withered heart.

One thing that strikes me about a lot of the talks is the value of a charismatic study system, by which I simply mean a clear cut relationship to nature. I think it is a weakness of my talks, and indeed of many other theoretical talks, that they fail to sufficiently highlight the organisms involved, treating the model systems as abstractions unworthy of particular merit or attention. The problem strikes me as twofold: on one hand I think that such naturalistic exhibitionism keeps the audience's attention better than sheer theory, but also reminds us of the tendency for nature to act in idiosyncratic and contextual ways.

Of course, the talks are only half the conference. Come nightfall there are always interesting people to talk to, and you really never know who you'll end up eating with. Never have I talked to so many people from so many countries.

Albuquerque out.

Summertime

Here in the northern hemisphere summer is in full swing, and for people of my age that means one thing: weddings. This past weekend a science-friend and I attended the wedding of a mutual friend, who is a rising star in the world of acarology, so naturally we ended up seated at the table with a bunch of other scientists. What ensued bore some resemblance to a mini-conference, with light banter about our research, and how we knew Wayne. Nautrally this entailed a trip down memory lane to my undergrad (Wayne and I were labmates during my honours project), when summer meant something very different - it meant field season.



Back in my younger days field season was a big part of science for me. In my undergrad I made massive collecting trips across Alberta, Saskatchewan, and the North West Territories (camping out on some collecting trips, and jumping out of helicopters on others), and during my masters I visited many lakes to gather inocula for my outdoor mesocosm experiment. Aside from providing the chance to be outdoors, an element of field work that I think we all like, this active field involvement also allowed my data to have at least a sheen of ecological realism. Both of these reasons make the call of the field beguiling, almost irresistable. The trade-off, however (there's always a trade-off...), was that it can be incredibly hard to assign any kind of mechanistic explanation to the complicated, ecologically-relevant systems that we often study in the field.



As a result I now spend less time outdoors, less time invested in ecologically relevant systems, and more time with 125 mL erlenmeyer flasks and two species diatom systems. In terms of data, things are lost (like the realism), but things are also gained (explanatory power and control). The same is true on a personal level: I've lost the sheer fun of playing in the mud and paddling madly to get off a lake before the thunderstorm hits, but I've gained the ability to engage in journal clubs, concerts, and movies during the soft summer evenings. And, who could forget, weddings.

Turbo Eco-jargon

Language is fluid and ever-changing, and the creation of new scientific terms can be useful if it makes the language more precise, but it also makes our work less accessible for those unfamiliar with specific literature and to the general public. When we start using overly specialised words as a substitute for more commonplace words, it becomes “turbo eco-jargon”.

An example of eco-jargon that works is the term ‘biodiversity’. It shortens ‘biological diversity’ to one word and still retains its meaning. However, most times we create and use terms that are not intuitive and/or not well defined. This can be especially problematic when terms have a common use, but a very specific scientific use, which may also differ among disciplines. Some examples are: stability, productivity, resilience, traits, and function(ing).

I am probably one of the worst in our lab for using eco-jargon (I was actually scolded by an editor once for my use of ‘turbo eco-jargon’ – his exact words!). But I like creating and using highly specialised words because I think they are fun.

Here are a list of some of my long-term favourite turbo eco-terms; how many do you know? (see comments for definitions)

• cursorial
• vagile / vagility
• phoretic / phoresy
• inquilinism / inquiline
• corticolous
• detrital

Currently I'm working on a manuscript to coin a new eco-term. I'll keep you posted!













Thanks to Biodude for feedback on this post. I look forward to your comments.

rockpool europa

At first glance it is not obvious what this is a picture of. I struggle with my poor photographic skills almost as much as I struggle with biodiversity, and yet these are still the kinds of pictures I take. I won't call it a metaphor.

The fact is this is a picture of a pool of freshwater on a rock face along the Finish coast, and it was teeming with cladocerans - tiny crustaceans that feed on pretty much whatever they can filter from the water column. Rock pools just like this one were made pseudo-famous (at least in the ecological world) decades ago by Ilkka Hanski and other researchers as textbook examples of metapopulations (spatially discrete populations of organisms that are linked by dispersal between the populations). When you pause to think about it, the concept is really cool. The pool is very isolated, may or may not be ephemeral, and yet it is packed with organisms. How did they get there? I occasionally remember that if we cut through all the technical jibber-jabber of spatial ecology, metapopulation ecology, and metacommunity ecology we are left with just such a curious question that could have been posed by anyone and interests everyone.

Many members of the Gonzalez lab, like myself, research nature in a fairly abstract way, tackling theoretical systems or heavily simplified model systems. There are all kinds of advantages to such approaches, but a minor tragedy that results from such minimalist science is a loss of the sheer wonder that you might experience 'out there' were to you stumble upon one of these pools on a morning's walk. The question is rhetorical, but how do we deal with the desire to pin down mechanisms that drive ecological processes, with the sheer wonder (and a skeptic might say incomprehensibility) of reality?

happy canada day all!

The littlest HOBO

“An hour in the field is a week in the lab” was the warning I was given as an M.Sc. student. Which means that Jon and I have enough samples to process for a year.

It has been a highly productive week. I can tell because I’m tired and sore all over. The snow has almost melted, and I escaped before the mosquitoes became too fierce. For the past week we have had a neighbourhood puppy follow us into the bush each day. We call her Georgia – she is very cute. She chases squirrels and takes naps while we measure nitrogen fixation.

P.S. The title of this post is somewhat of an inside joke, as we use HOBO dataloggers to record temperature & relative humidity year-round at the experimental site.  "The littlest Hobo" is also a mainstay of Canadian family television from the 1980s, featuring a wandering dog who helps everyone he happens to meet during his wandering.  Thanks for the company, Georgia.

Snow

Jon and I survived the 2 day trip to our northern Quebec field site near Schefferville.
This morning we left the McGill sub-arctic field station in almost all the clothes we brought, and my feet were still cold by 9:30am.




What can we say, there was a lot of snow.  The upside is that there are no bugs.

Where is Schefferville, Anyway?

Cross-posted from my other blog

Yes, I'm spending the next 2 full weeks at the McGill Subarctic Research Station in Schefferville, Québec, sampling my field experiment with moss & their associated micro-ecosystem. And the most common question I get is: “Where is that?” *sigh* If only I'd found a reason to do research at the Bellairs research institute in the Barbados, I might have avoided this question :P

Schefferville is in northern Québec, near the border between Québec and Labrador. So close, I could easily walk to Labrador in a few hours from town. Getting to Labrador City would take a little longer ;-)

Vital statistics:

• 54º48'00” N, 66º50'00” W
  
• Government of Canada Topographic Map reference: 023J15
  
• Declination as of 2009: 23° 9' West
  
• Population as of 2006: 202 (actually closer to 800-1000 people in town)
  

Formerly known as the town of Knob Lake, Schefferville was home to a mining community until the iron mine closed in the 1980's and most people left. It has since been a destination for hunting, fishing, and other outdoor activities, facilitated by the outfitters based in town. There is, however renewed interest in iron ore mining in the area, though not by the same company that built the railway. As far as I know, Schefferville has one school, an arena, sports field, one general store, a hardware store / snowmobile repair shop, a combination Dépanneur & SAQ Express (alcohol counter), much of it owned by the same man. There are also at least 2 bars in the area, although I was told not to go to a certain one unless I wanted to get into a bar fight. The airport is actually much closer to town than the train station, although there is a taxi from the train. It doesn't look like one, and is in fact an old ambulance past it’s prime, but you can ask around and someone will point it out when it comes.

I've been impressed with the depth of the scenery here: the land and the sky have a distinctly more three-dimensional appearance and feeling than in an urban environment. Even the sky has more depth than I remember in Vancouver, with usually at least 3 layers, making for some striking and beautiful sunsets.

I made a little flyby tour of the area in Google Earth, including my study site. I am such a nerd.

Why Biodiversity?

Living systems are repleat with variation at every scale and level of organization.  We are interested in how such diversity is maintained (coexistence), and what the consequences of varying levels of diversity are for system dynamics (process rates, functioning, stability).  

How many species are needed for a system to persist for multiple generations? 

How many species can survive without going extinct in areas with limited resources? (coexistence)

How does the number of species affect ecosystem processes such as productivity, stability, or other measures of functioning?

How do ecosystems respond to environmental changes or other external forces such as pollution, fragmentation, or climate change? (stability, resistance, resilience)

How do evolutionary processes affect ecological patterns and processes and vice-versa?

Gazing at Gaia's Navel

On a more philosophical note, studying biodiversity sometimes feels like "navel-gazing", while you are studying minute details of an immense biosphere, of which we are a part.  But, it's like looking at Gaia's navel, which so much more interesting than your own.

A diversity of reasons

Although our lab shares some common approaches to studying biodiversity, we each have our own personal reasons for choosing to work in this field.  We invite you to post your personal reasons in the comments section of this post.

Off to Schefferville

Bright and early Sunday morning.
Jon (Biodude) and I are off to the Schefferville field site today. We have an 11am flight from Montreal through Quebec into Sept-Iles around 4pm. Tomorrow we take a 12-hour train from Sept-Iles north to Schefferville.

I plan to collect lots of moss; Jon hopes to measure lots of N-fixation, and we are both generally looking forward to enjoying the sub-arctic summer experience. Did I mention it is supposed to snow there tomorrow? Ah well, maybe it'll keep the bugs down.

Have a great week everyone!
-Z

What is biodiversity science?

It is the discovery of the patterns and processes that describe and explain the diversity, distribution and dynamics of life in the biosphere. 

This is a formidable scientific enterprise because there are many more organisms on Earth than there are stars in the Milky Way! 

(Apparently there are ~100 billion stars in our galaxy) 

All those organisms are split up into many different species each of which is represented by a few hundred populations.

(Our best guess is 10-15 million different species, each with ~200 populations on average)

What motivates much of the science in our lab is the alarming rate at which populations and species are disappearing. 

Biodiversity scientists are being challenged to understand the inner workings of the biosphere whilst human society subjects it to new combinations, rates and levels of environmental change.

Where are we?

A bunch of us from our lab decided to start a blog. A blog about stuff going on in our lab, but not necessarily serious academic topics. More like quirky thoughts and comments about academic stuff, or social events.

Our first challenge is to choose a name to put up in the URL so readers can find us. We wanted a name that was:

• related to biodiversity science (our main field and area of research)
• quirky or silly
• but not totally unprofessional or inappropriate

It's a fine line.

Our leading contenders so far are:

• sourcesink
  • already registered, but the blog was removed :(
• ecodrift