From Pine Beetle, Mr. Opportunity?, The Tyee

“Our forests are in transition,” said Jim Whyte, director of operations at the Provincial Emergency Program. “We’re moving from healthy green forests to dead forests.”

This week’s insightful analysis is for Naeem et al’s sweet 1995 paper on their ecosystems-in-boxes experiment at the ecotron, in which they manipulated species diversity in producer-consumer-predator systems and measured ecosystem functions for 200 days.

The original paper: Empirical Evidence that Declining Species Diversity May Alter the Performance of Terrestrial Ecosystems, Philosophical Transactions of the Royal Society: Biology, 347(1321) 1995.

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An “insightful analysis” for the longly titled Which species? What kind of diversity? Which ecosystem function? Some problems in studies of relations between biodiversity and ecosystem function, Bengtsson, J. 1998. Applied Soil Ecology 10: 191-199.

Bell ringers: The sentences which most excited me were

1. “Diversity of functional groups, diversity within functional groups vs. total diversity”

(p.196) Despite the author’s claim that diversity is not a mechanistic driver of ecosystem function, it seems clear that we will identify any real mechanisms linking ecosystem function to gritty biology through the persistence of statistical correlations between units of stuff in ecosystems and the outcomes of those ecosystems. Divvying up diversity into inter- and intra-functional groups measures seems like a powerful step in finding the most suggestive statistical correlations.

2. “It is difficult to predict which species will be of importance in the future.”

(p. 197) I gather there is a good literature on this “natural insurance capital” theory, which is an exciting idea. Clearly there is a Gleason:Clementisan evolutionary component to the question of whether any given diversity of groups/species is best suited to the likely perturbations of their locale. It seems to contradict the author’s claim that “there is no mechanistic relationship between diversity and ecosystem function”. Perhaps not in the immediate term, but given the convincing argument for a consideration of time-dynamic processes, all ecosystem functions may be dependent on a future-proof “smart diversity”.

Mechanism and correlation: The author is clearly not a disciple of R.H. Peters and his “Critique of Ecology”, which advocates an abandon of mechanistic “narrative descriptions” (which Peters claims can’t predict outcomes or definitively answer questions). Rather, the author suggests correlation is a lesser kind of knowledge and that mechanism is the goal of real beef-eating scientists. I agree with him, but wonder if he’s forgotten that we get there through data, and if we pre-judge our data based on the existing canon of identified mechanisms, we may miss out on new candidates. This is especially important in an emerging field, where there may not be consensus around relevant mechanism. A bunch of possible ecosystem functions are listed, and there is an implication that those functions plus some other stuff that we also know are a good approximation of what ecosystems do. My intuitive response is that ecosystems are awfully complicated and our understanding of how they work is yet basic. I fully agree with the author that we’ve been way over-focused on divvying them up into units of species, but I’m skeptical that we now know how to best aggregate them.

Experiments and data aggregation: The kinds of experiments the author advocates for testing mechanism are awfully compelling (and perhaps I should more carefully read the ecotron paper now). They would be tough though. Time-dynamic-analysis, controlling for biomass, in real ecosystems when possible, is a high bar. Perhaps rather than insisting on defining “functional groups in consistent ways” a priori, we should be working on measuring our data at the least-aggregated level, and providing it in standardized formats into open repositories which would allow us to take on such cool-but-daunting studies in the “big science” format increasingly popular with the bioinformatics/molecular genetics crowd.

I’m really excited about one of my new classes this semester. NRE 639-039, Don Zak’s ecology seminar, entitled “Biodiversity & Ecosystem Function: Are There Any Links?”. After having taken a rather more technical course last term on measuring and storing data on biodiversity and ecosystem informatics, I was left asking myself over and over if biodiversity was really a monolithic good and if for instance, there were any links between biodiversity and ecosystem function. I’ve become an evangelist of function and raw physical mechanism as a relevant focus for ecosystem study, especially as opposed to our Victorian-artifact fetish with whatever species are.

So oh boy this otta be a good course, the kind of course you say, carve out a chunk of your life to go to graduate school for. Dr. Zak is consistently rated by his students as a great instructor, just as an added enticement. He’s asking for a weekly “insightful analysis” response one-pager to one of the papers we read. Putting the adjective “insightful” in the title of the assingment seems optimistic, but opt ism is good and I’m sure we’ll all do what we can. I’m inclined to treat them as a sot of blog thing. So I’m going to post them to my blog, natch. The first one is the next entry. Yay!

The One-Laptop-Per-Child computers are going on sale to non-developing-country-children starting Christmas (maybe) for a few hundred bucks each. These are small, ruggedized, weather-sealed, open-software-driven boxes explicitly designed for mesh networking. Does this have implications for people looking to deploy sensor networks for ecological monitoring?

The machines will be priced well over production costs, as the sales are meant to subsidize the give-aways, but the price will still presumably benefit from the economies of scale embedded in the massive production runs they’ll be working with. Especially compared to the cost of building your own batches of custom sensor boxes.

The green-and-white, kid-friendly laptops that can be powered with hand cranks were designed for use by poor children in the world’s impoverished nations. They were designed to withstand severe weather common in areas of Asia, Africa and Latin America. They run on Linux software, feature a high- resolution display that can be read in direct sunlight and are known for their low power consumption, operating up to 12 hours on one battery charge.

If you’re interested in the tension between correlation and causation in ecology and don’t feel like standing up, it turns out that great chunks of R.H. Peters’ “A Critique For Ecology” is available online in Google Books. Apparently Cambridge press is experimenting with sticking big swaths of its books up on the internet. It makes a lot of sense to me: it doesn’t cost them anything, and there is no way I would actually sit and read through all of a book on a computer screen. Ouch. But on the other hand, I’m at least ten times as likely to buy or otherwise get a hold of a physical copy of the book if I read a bunch of it first. So there you go.

If it sounds like a boring topic to you (causation v. correlation etc) it may be, but if you’re interested in ecology it may not. Peters argues that ecology’s obsession with explaining the whys behind the way things are in nature has led to a vague and muddled science, given that it’s functionally impossible to prove why something happens. In his mind, ecology goes around identifying problems and never really solving them, so the longer it exists as a science the less we seem to know. He points out that if you want to contribute to solving problems you have to be able predict what will happen in the future given the current state or possible current states. And prediction is all about correlation, which is a separate issue from causation. He thinks we need to be worse natural historians and better statisticians.

It’s an interesting argument, but childish and silly of course. Which is obvious if you read the book. Which, hey presto, you sort of can!

A Critique for Ecology By Robert H. Peters

I have a group project writing an agent-based program to simulate the foraging behaviour of ants. The NetLogo implementation of this idea makes it look easy. Turns it out it’s not. Which has lead to lots of interesting questions about ants.

Incidentally, the project is being written using the RePast agent based modeling libraries for java. Now, I haven’t looked at the code of the NetLogo sample implementation since I started writing this thing, because we’re not supposed to. But I did look at it last semester, and I seem to remember you could fit the code on a tshirt, using a fairly hefty font, if you were so inclined. You could not fit the equivalent java code on a tshirt. You could not fit it on a muumuu. If nothing else, this project is convincing me that as soon as we’re let loose, I’ll be switching to NetLogo. RePast may not be as clumsy or random as a blaster, but NetLogo is just like way faster. Bring on the clumsy and random.

In an effort to answer some of my questions about how real ants have solved their RePast programming issues, I got a copy of Ants at Work by Deborah Gordon out of the library. I was shocked and mildy irritated to see that no one has checked out this copy — the only one in the UMich system — before me. WTF? I first read AaW when I was contemplating a project for my final year field course in undergrad, and it sticks in my memory as one of the most interesting books I have read. Dr. Gordon studies how it is that individual ants, obeying no rules outside of their own tiny heads, somehow come together to form the persistent yet adaptable superorganism that is an ant colony. She uses methods ranging from painting individual ants to digging up colonies with backhoes. It was my first introduction to the idea of emergence, before I (or apparently Dr. Gordon) had ever heard the word.

I can’t believe nobody else has read it around here. What’s wrong with these people? It’s so much more portable than The Ants, and costs 1/20th as much, even if you don’t include the cost of the hand cart.

Also, there is a raccoon sleeping in the garbage bin to the east of the Shapiro library doors.