I gave a presentation of my research on southwestern plant patterning yesterday–this was in fact an “oral dissertation defense”, according to the Masters Project Handbook. Below is a video, and the slides. I’ll hopefully be adding more material to the research page as I get around to it, including a NetLogo implementation of an existing vegetation model and possibly a Google Earth tour of some of the sites and data. First however I have to finish writing the non-oral part of the thesis.

Slides (6mb pdf)

Narrative summary of the talk:

Self-patterning of vegetation has been identified in dryland ecosystems worldwide, such as the “tiger striped” savanna of the African Sahel and the banded shrublands of Australia. In these water-limited systems plants are organized into consistent spatial structures by the facilitation of new growth in the organic shadow of existing plants. These landscapes are theorized to be more efficient at retaining rare rainfall, but are also expected to undergo catastrophic shifts if precipitation drops below difficult-to-predict thresholds.

No such banded systems have been identified in America, but I was curious if more subtle patterning could be happening in southwestern drylands which share many of the same ecosystem characteristics and display threshold response to changes in precipitation. If a form of emergent patterning were occurring in these ecosystems, it would have implications for predicting landscape response to pending changes in climate. Focusing on pinon-juniper woodlands in Arizona and New Mexico, I mapped the shapes of patches of vegetation from aerial photographs and measured their degree of spatial pattern. Estimates of surface water movement and distribution were developed for the same sites from digital elevation models. Testing the spatial correlation of these landscape characteristics indicated strong linkages between vegetation patch shape, vegetation density, and surface water hydrology. In sites in Arizona, these relationships were consistent with theories of self-patterning, suggesting that this previously unidentified phenomenon could be occurring in in an American dryland landscape.

Where i is a very large patch class; n is the very large number of patches of class i; j is the very large number of patches of all classes; p is the very large perimeter of patch ij; and a is the very large area of patch ij.

I’ve updated my research plan, again. It’s becoming a hobby. Now with improved narrative, and references to attest to its scholarly character.

2 months ago I was wandering around in rented cars, waking up to the dawn in improvised Forest Service campgrounds, cooking up bacon and eggs and coffee on camp stoves, breaking down my tent then rushing out into the piñon-juniper woodlands with a gps antenna magneted to my bandanna, a compass around my neck and a camera in my hand, documenting the landscapes that were going to become my study sites. I would drive and hike around in a rush to look at things until I decided I had to look at something in particular very slowly. Then I would stare at it. Mostly bushes and trees and soil and water courses. Also hills and valleys. I visited Sierra Vista and Tombstone and Arizona and Flagstaff and Cedar Ridge and Tuba City, and mostly places in between, like Cochise County and the San Pedro River and the Coconino forest and Waputki and the Little Colorado canyon and the rangelands of Navajo Nation. I took a train to New Mexico and did similar things there. Then I took a train home. It was a good time. There was a lot I missed because I was in a hurry to look at semi-arid vegetation, but there was a lot I saw because I was looking for semi-arid vegetation. I wrote about it a bit here.

Because I had a camera in my hand and because New Mexico and especially Arizona are so damn visual, I took a lot of photos. I’ve finally posted some of them up here.

I’m pleased to see that my research has started to produce some GIS art.

Below: Coconino Juniper Patches with Landscape Shape Index Overlay. Media: Patch Analyst on isodata classification of 1m orthoimagery.

For the curious, I’ve posted a more detailed version of my thesis research plan. Which is currently being executed.

Also, I’m nearly done developing some of my photos from my summer research trip, and that gallery will be up soon.

Chris Darimont is a wolf researcher who used to hang out with some of the people I used to hang out with in Victoria. As a wolf researcher, he claims traditional pride of place amongst the tribe of ecologists. As such, your contemporary future-looking ecologist might be tempted to disparage him as a megafauna fetishist, but I gather he actually does some interesting, post-Mowat research.

So it’s nice to see that the Government of Canada has equipped him with an NSERC grant and posted him off to Southern California. Other NSERC fellows I have known have found great success in these United States before returning to enrich the Dominion. And Chris is drawn towards the human side of the picture, so good luck with that, I’ll follow when I figure the I’m up for it.

After getting irritated at humankind’s inability to accept that some things are genuinely uncertain, I open my podcasting device and hey presto:

Resilience: Adaptation and Transformation in Turbulent Times — A World Of Possibilities, May 6th

It opens with Buzz Holling (who NRE 580 alumnus will remember for panarchy theory) on adaptation, uncertainy, adeterminism, non-equilibrium, and such like in the general world. Then it moves onto Brian Walker talking about much of the same in ecosystem management, plus control fetishism. Then it moves on from there. Recorded at a Stockhlom conference on applying biology-based resilience theory to social systems. The idea of which is now creeping me out. Except that maybe, just maybe, this is a group of people that can be trusted to think rationally across disciplines. Maybe. Anyhow, it’s good listening.

Brian Walker’s talk reminded me of a lecture on conservation management from my undergrad, wherein Thom Nudds announced that if you manage to get an ecosystem to not cycle you’ve flatlined it, so congratulations on that.

Here’s a fun bit of Google Earth-utilizing research:

Magnetic alignment in grazing and resting cattle and deer, Begall et al, PNAS

“We demonstrate by means of simple, noninvasive methods (analysis of satellite images, field observations, and measuring “deer beds” in snow) that domestic cattle (n = 8,510 in 308 pastures) across the globe, and grazing and resting red and roe deer (n = 2,974 at 241 localities), align their body axes in roughly a north–south direction.”

Apparently this work follows on from previous research the team has done on the sensing of magnetic fields by naked mole rats. In this case, they used Google Earth to scroll around looking for cows, then once they had documented 8510 of them, decided they tend to lie down facing north-south. And likewise for deer.

Here’s some more from NPR.

“Holland says that other researchers should confirm the finding. One way of doing that would be to “start going out and putting magnets on the heads of cows and horses and deer, to see how that affects them,” he says. “That’s one of the more traditional ways of testing if they have a magnetic sense.”

If they really do have an internal compass, he says, the magnet would mess it up.”

I’m back from my two-week ramble through the public lands of Arizona and New Mexico. This was an ideal destination for me: I’ve been in the area a few times before, just enough to begin to know what to seek out and what sorts of landscape patterns might be waiting for me, but not nearly enough for it not to seem entirely exotic and impossible to my boreal-based brain. Well, I’ve only now scratched the variations on landscape and vegetation and physiognomy of the great American southwest. But I did get to run down some old leads and spend some really solid time in a couple of regions I’ve long wanted to. And do so with the wonder of ignorance.

And oh yes, I was there to do some research reconnaissance. Looking to see what vegetation pattern looks like from side-on and roots-up instead of from above. I have a lot of digesting to do, but I suspect the trip was successful on that criterion. For sure I had great meetings with people who really do know the ecology of the magnificent semi-arid zones: Dave Breshears (who made time for me the day his right-hand-guy was leaving for a faculty position), Neil Cobb (who made time for me the week he was prepping for his wedding celebration) and Michaela Buenemann (who made time for me in between settling into her new faculty position and road tripping to Dr. Cobb’s wedding celebration). The reflexive generosity of time and ideas that researchers have for each other is one of the things I love about working in the sciences. It seems the best people are the ones who are the most giving of their resources. (Including data! Thanks guys. Thanks also to Dr. Alfredo Huete, whom I now really regret not having been organized enough to ask for a meeting with.)

Thanks also to this guy, whose website drove home the point that, unless it specifically says “no camping”, you can pretty much camp anywhere you want in the southwest. This turned out to be a key idea in my trip. There were a lot of places I wanted to camp, and did. And while I’m at it, thanks also to Enterprise, for not freaking out when I brought some rental cars back with a little dust in the wheel-wells.

Much of the point of being there was to take photos I could later reference while taking the remote-sensing god’s eye view of the same landscapes. So I had my camera in my hand a lot, and I’ll post some photos as I work through them.

I’m leaving today for 2 weeks of field work in Arizona and New Mexico.

I’m doing some field reconnaissance in support of my weird thesis research on self-organizing plant patterns in the semi-desert. That mostly means I’ll be driving around in rental cars, looking to see what the places I’ve been peering at from above actually look like in person. Also camping out in the high desert at night, looking to see what patterns the stars have. I’ll be in the Tucson/Sierra Vista region, then north of Flagstaff and up to the rim of the Canyon, then training into Santa Fe/Los Alamos area. I’m taking the Southwest Chief back to Chicago and Ann Arbor on the 23rd.

Do you see a pattern? I don’t see a pattern.

I’m trying to find some additional study sites for my research. I’ve recently realized how stupid I’ve been by not using Google Earth as my main exploratory site-search tool. Way way waaay faster than trying to download overview imagery raw from USGS or wherever. It also occurred to me that there are thousands of people who cruise around in Google Earth every day, looking for interesting things and talking about it in the forums. So I posted there, in case anybody might have seen the kinds of semi-arid plant patterns I’m looking for. I’m interested to see if there will be any response.

update: the post has been moved to the “Moderated” section of the Nature and Geography forum. The above link has been updated.

A study site in Arizona.

Somebody had to do it: a firefox extension to make every youtube video Rick Roll instead.

rolltube

I recognize there has been a lack of substantive posts around here lately. Several good ones have come and gone in my head, but it’s been a busy time and there hasn’t been an opportunity to type them down. If you want interesting substance, I’d recommend reading this Q&A regarding the Bear Stearns situation and contemplating how a system that is so fragile that a single failed node in the network can threaten its total collapse is going to fare when the recursive effects of global climate change perturb it from many angles simultaneously.

Or just install that rolltube extension and surf the video net!

Two good stories:

The passing of a Yellowstone Cinderella, High Country News

“She was one of the original 31 Canadian wolves transplanted to Yellowstone to kick off the wolf restoration effort in the Northern Rockies. Much of the park’s spectacular wolf recovery can be attributed to her breeding success: At least three of her daughters have gone on to form their own packs. And not only was she the alpha female of the largest wolf pack ever recorded — the Druid pack numbered 37 wolves in 2000 — but she also contributed mightily to our knowledge of wolf behavior and pack dynamics.
….
Doug Smith, the Wolf Project biologist for Yellowstone, says, “None of the other wolves liked 40 so they would hang out with 42 instead. In fact, the only wolf to visit 40’s den was 21.” When the aggressive 40 threatened her sister again, Smith said, “This time 42 said, ‘forget it’ and attacked 40, defending her pups. At least two other wolves joined in and left 40 a bloody mess.”
….
The next day 42 moved her pups clear across the Lamar Valley, took over 40’s den and raised her sister’s pups along with her own. She quickly assumed the alpha role, which she held until her untimely death this winter.”

Jump the Shark, New York Times, about the demise of professional pool sharking.

“But that’s just gambling,” Mr. Bell says wistfully. “Real hustling — driving to a pool room in another state, walking in, setting the trap, busting the local guy and then heading to a new town — is different. That’s what ain’t there any more.”

The New Yorker has a gigantic piece up on Paul Watson, the former Greenpeace cofounder who is now the generalissimo of the Sea Shepherds. Watson is possibly the last of the fully mobilized alpha-male environmentalists that roamed the heroic early age of the green action movement. His ego spreads out across the sea, like a living shield for the dieing oceans. Say what you want about him and his mythic vigilantism, ramming a decrepit Norwegian trawler with a jagged cutting boom welded on the side into an active whaling ship denormalizes the situation for everybody. And I think we need a lot of that. It’s not real clear that many people have actually gotten hurt by his actions (although some certainly could have, and apparently some have come awfully close). Anything that slows up the sterilization of the oceans, which may be heading towards an unrecoverable threshold, or at it, or just possibly past it, is a good way to spend a life.

Neptune’s Navy, Paul Watson’s wild crusade to save the oceans

I also thought this was an interesting point:

It was not until the mid-nineties that fisheries scientists turned their attention to the spiral of exploitation and attempted to gauge its consequences. They discovered that their discipline had been measuring biodiversity with a very narrow lens: looking, for instance, at habitats only in a particular region of the ocean, or at the rise or decline of a particular species, and usually with respect to benchmarks that had been set just decades earlier. No one had tried to determine what the full spectrum of life in the ocean looked like a hundred years or five hundred years in the past. “We forgot the wonder and splendor of a virgin nature,” Watson wrote recently. “We revise history and make it fit into our present perceptions.” In 1995, the process of forgetting was given a name—“shifting baseline syndrome”—by Daniel Pauly, a scientist at the University of British Columbia. “Essentially, this syndrome has arisen because each generation of fisheries scientists accepts as a baseline the stock size and species composition that occurred at the beginning of their careers, and uses this to evaluate changes,” Pauly argued in the journal Trends in Ecology and Evolution. He concluded, “The result obviously is a gradual shift of the baseline, a gradual accommodation of the creeping disappearance of resource species.”

This week we gave the insightful analysis treatment to Wardle et al’s 1994-97 experiment in a New Zealand pasture, in which they removed all the species from 360 20cm patches and allowed them to grow back in, while selectively pruning out different mixtures of functional species groups. Good stuff. Especially cool was their careful measurment of below-ground biota and below-ground ecosystem functioning. Especially especially cool was the fact that they collected a time series of data across the 3 year times span of the experiment. Most of these diversity experiments have to destructively sample to collect their data and so they end up with a single snapshot of the state of the ecosystems at the arbitrary end. These folks sampled just a few of their plots per time step over a bunch of steps, so they had lower sample sizes at any time but a real dynamic story to study.

The paper itself is a whopper, 34 pages in Ecological Monographs.

David A. Wardle, Karen I. Bonner, Gary M. Barker, Gregor W. Yeates, Kathryn S. Nicholson, Richard D. Bardgett, Richard N. Watson, Anwar Ghani. Plant Removals in Perennial Grassland: Vegetation Dynamics, Decomposers, Soil Biodiversity, and Ecosystem Properties. Ecological Monographs, Vol. 69, No. 4 (Nov., 1999), pp. 535-568, doi:10.2307/2657230

scholar.google link

Thankfully the insightful analysis is the usual one page, below the fold.

Read the rest of this entry »

This week’s insightful analysis: from 1997, Michael Huston critiquing Naeem et al’s ecosystems-in-boxes experiments (insightfully analyzed here). Huston claims that the Ecotron experimenters dropped the ball by building in an inevitable bias towards a wide range of plant sizing in their high-diversity boxes, and further claims that debunks the diversity-ecosystem function link. He brings some big-gun databases of plant survey data into the act, and proposes the way forward. I think he’s got some good fundamental points, but then goes too far. Mostly I think he’s got a pretty trivial idea of what “function” means, which makes his claims that Naeem et al’s results are trivial sound a bit whiny. But I don’t say that in my analysis, because I’m nice. Is there anything more heart-pumping than scientific debate?

The paper:

Hidden treatments in ecological experiments: re-evaluating the ecosystem function of biodiversity. Huston MA. 1997 Oecologia 110:449-460. (Don’t issue and volume citations look weird on the internet?)

Text of the analysis after the fold.

Read the rest of this entry »

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.

Read the rest of this entry »

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.