The Dark side of diversity

Recently Pärtel et al. (2010) introduced a simple but intriguing idea that the fraction of 'missing' species from a site provides insights that can be used to understand biodiversity loss.

In cosmology dark matter is thought to make up the dominant fraction of the matter in the known universe. Ordinary matter, the stuff we see, makes up a small fraction of total matter. Can the same be said of species diversity at a given site? The authors of this paper define dark diversity as the fraction of species we do not see at a site but are potentially capable of inhabiting it within the regional pool. Ecologists have long known that local diversity is typically a small fraction of the total diversity in the regional pool, but few have focused on quantifying the variation in dark diversity from site to site. A global analysis presented for plant diversity reveals interesting spatial patterns in dark diversity. In particular, dark diversity is relatively lower in temperate regions where 'ordinary' diversity represents a greater ratio of the total potential pool than in many parts of the tropics. 

The value of the concept can be seen when we ask whether dark diversity in a locality is increasing rapidly over time, in particular, because of local extinction due to human disturbance. As long as dark diversity is high the potential for ecosystem restoration remains. However, extensive and persistent extinction would also erode dark diversity, and eventually reduce the options for restoration; a worrying possibility for many areas of the world. 

The authors offer some advice about how to decide whether a species can potentially inhabit a site but this is a nontrivial decision. For example, many species may persist as sink populations. By definition these species could not exist in a community in the absence of immigration. The only way to measure this component of local diversity is to isolate a community. Should sink species ('shadow' diversity?) be excluded from consideration? These and other questions arise when thinking about dark diversity, but this does not detract from the value of the concept. This notion is ripe for theoretical analysis.

Reference:

Pärtel, M., Szava-Kovats R., Zobel M. (2010) Dark diversity: shedding light on absent species. TREE online early.

Free conservation biology textbook: Conservation Biology for All

Free conservation biology textbook: Conservation Biology for All

How can you say "no" to a free book, especially when it includes chapters by some of the world's most prominent ecologists and conservation biologists?!

In honor of the international year of biodiversity, Oxford University Press has made this book available as a free download. Get your copy today! We think you'll enjoy it.

The downside of blogging

I was recently at a dinner party where I was talking to a fellow who was very anti-blogging. His position was basically that communication is context dependent, and the internet is the antithesis of context dependent communication. I'm sympathetic to his position; in a broad, context-free setting like the internet I think it is nearly impossible to make statements that aren't somehow naïve or asinine, and as a result I have been increasingly attempting to communicate with images. I have always appreciated Barthes' assertion that photos say nothing more than "this has been," and I find the notion that photos offer a 'silent discourse' attractive, or at least intriguing (thus my fascination with Edward Burtynsky's pictorial/textual ambivalence to ecological disaster). Ultimately, however, I acknowledge that attempts to communicate with images are no less naïve than attempts with text in the internet's context free environment. Images without textual anchors may be considered silent in one sense, but, as Susan Sontag has noted, in another sense they make extremely loud ethical statements. Finally, even if images could be considered truly 'silent', there are hefty ethical implications to the act of silence.

I started this post describing a personal conversation about the importance of context in conversation. Ironically I have now transported that conversation's content from a closed-format communication into an open-format communication (this blog). If I have done so I think it must be because I still believe there are important things we could be saying to people outside of our immediate spatial and social environments, and one of blogging's strong points is that it allows us to do just this. So here is my resolution for this blog: to return to textual communication, and to speak to whomever wishes to listen. Just don't take what I write out of context.

Why We Blog

The Ecodrift blog has been quiet lately, but there's been a lot going on in our lab: PhD students defending (hopefully, that will include me someday), new students joining the lab, and the launch of the Quebec Centre for Biodiversity Science.

In my own little corner, I've been learning a lot about R while coordinating a series of statistics workshops in R for our department. I hope to post more about this soon, but I've been thinking a lot recently about my workflow in R, and how to organize all my files (aka Project Management).

While reading other blogs about R and workflow, I found a link to Drew Conway's list of ten reasons why grad students should blog. Hey! We're grad students (& Post-Docs)! We Blog! Ok, we share a blog, but this has advantages over trying to forge an individual identity on the web:

• We can provide more content as a group than individually
• We don't have to try to compete for readers' attention: because there really aren't enough blogs already out there (*sarcasm*).
• We can collaborate on content, or provide direct feedback, even having discussions all in one place!

Why do members of our lab blog? Many of the reasons mentioned in Drew Conway's list certainly apply, but I would add that it also serves as a record of progress along our scientific journey in various areas: snapshots of how we were thinking at the time. Like an academic paper, but less rigorous and not peer-reviewed (and therefore faster but less reliable). It reminds me of a McGill yearbook I recently found from 1978 in Thomson House, including a summary of News from that year, and major events on campus: I was struck my how little some parts of lower campus have changed even since then (McGill is OLD), and how much the fashions and administrative issues have changed. There was an article from one professor predicting that the paper publishing business was going to get too expensive, compared to microfiche cards that cost pennies and could easily be used by students with a microfiche reader for a mere $100! Ok, maybe he hadn't heard of the internet yet, but that just goes to show that even expert predictions often fail. I prefer to stick to explanation rather than prognostication, but Your Mileage May Vary.

Scientific knowledge is characterized by historical facticity, and today's truth may become tomorrow's urban legend: do we act on what we know, or keep waiting to resolve uncertainty? Blogging provides a record of the thought, reasoning and discussion process that eventually turns into peer-reviewed publications, media reports, etc. and becomes part of the public record. So, blogging provides more fodder for historians and philosophers of science and provides people a peek into the developmental process of "Scientific knowledge".

This also suggests another reason to blog: to spark philosophical discussions that are difficult to publish in a forum read by scientific peers. It sometimes feels like scientists take the philosophical aspects of their work for granted all too often, despite a few of us jumping up and down about how your philosophical approach can affect the way you interpret results, or even the questions that you ask in the first place. Science - at least academic science - is just as social and cultural as it is academic. I may not have anything novel to say about it, but it is something that occasionally bears repeating to provoke thought in others.

So, blog away my fellow Biodiversity Scientists, and join the party. I'm waiting for you to blow my mind.

Life as a Postdoc

After several years of jobs being scarce, this year has been promising for those of us looking for a full time job in academia. But interviews have come and gone, and no golden ticket yet.

I am preparing for my next interview which includes not just the job talk, but also a chalk talk. I’ve never seen a chalk talk, and as far as I can tell, it is like a round-table discussion on your future research projects, but with timelines, goals, and funding strategies outlined on a board. I’m terrified.

I have plenty of preparation done, as I’ve though a lot about my future research and success of my lab, but mostly it’s in the form of written proposals. And it’s written down for a reason – 2 actually – firstly, I have a horrible memory, and second, I’m a better writer than I am a salesman.

The fact that this interview is also in the States means that there is a whole other level of insecurity; not being totally sure of how NFS grants are awarded (versus NSERC), what grad student culture is like, or what do you do for 3 months if you have a 9 month appointment.

The lab has been great in supporting me though. On Monday many Gonzalites showed up to eat donuts and hear my job talk. If only the hiring committee could be bought as easily. Mmmmm donuts!

Trade-offs, and the value of Diversity

Researchers in Budapest recently formulated an explanation for why horses might want to be white (from an evolutionary perspective). White horses are more susceptible to skin cancer (of all things) and predation. Well, they do stand out, so higher predation risk isn't too surprising.

But, it turns out the white coats reflect less polarized light than dark horses, which actually makes them less visible to horseflies. Hiding from one risk, while exposing themselves to others.

This story caught my eye, because it highlighted a few aspects of diversity ecologists have been mulling over for a while now. Different traits within a population often trade off between adaptation to one selective pressure (predation, drought, resource depletion, etc.), at the expense of greater risk from another one. These trade-offs can allow a diversity of traits to persist within a population, so long as each experience positive fitness on average.

This is similar to the arguments proposed in the insurance hypothesis by Michel Loreau and Shigeo Yachi, but applied to individuals within a species, rather than species within a community. But the net effect is the same: stabilization and reduced extinction risk at higher aggregate levels of organization. Individual-scale variation may also play an important role in species coexistence at the community level.

Do trade-offs drive evolutionary and ecological dynamics? Do they promote diversity at all scales?

In other news, danish & japanese researchers found yet more evidence that Biology is freaky. They were able to show that changing the concentration of oxygen in water above sediments devoid of macrofauna, directly led to changes in hydrogen sulfide concentrations more than 12 mm below the oxic zone, mediated entirely by electron transfer between bacteria through the sediment to the surface (interface with the overlying water column).

In other words, the bacteria in the sediment created an electric current to drive cellular metabolism and use molecules millimeters away as electron acceptors! That's like running while being powered by a battery sitting a mile away in your house!

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.