‘SCALING IN ECOLOGY’ AND THE ESA 100TH ANNIVERSARY – SYMPOSIUM ON ‘A FOCUS ON SCALING FOR THE NEXT 100 YEARS’Posted: February 2, 2015
“Biological research is in crisis…. Technology gives us the tools to analyze organisms at all scales, but we are drowning in a sea of data and thirsting for some theoretical framework with which to understand it.”
– Sydney Brenner. 2012
“The harmony of the world is made manifest in form and number, and the heart and soul and all the poetry of Natural Philosophy are embodied in the concept of mathematical beauty.”
– D’Arcy Thompson 1942
I am happy to announce that we will be organizing an exciting and synthetic symposium at the next Ecological Society of America meeting – the 100th anniversary of ESA! The symposium is entitled. “Scaling in Ecology: Building a synthetic and predictive science for the next 100 years”. This symposium brings together a collection of scientists working at the forefront of efforts to integrate patterns and processes across scales.
Why a symposium on scaling?Probably the most central problems associated with ecology is “how do we understand and ‘scale up’ ecological pattern and process from genes to ecosystems?” and “how do we predict the response of organisms, diversity, and the biosphere to climate and land use change”? Ecology for the next 100 years will increasingly need to address the challenge of quantitatively linking pattern and process across temporal and spatial scales as well as how to scale up biological measures and theory to predict the effects of climate and land use change. This is a grand challenge – it has been for the past 100 years of ESA but certainly will continue to be for the next 100 years
Two of the most influential ecological publications from ESA have been associated with the problem of scaling – indeed, these papers have been the ESA MacArthur Award papers by Simon Levin (The Problem of Pattern and Scale in Ecology) and J.H. Brown (The Metabolic Theory of Ecology).But how much progress have we made since these papers? A focus on scaling has always held the promise of providing a synthetic framework through which to integrate and understand the processes responsible for generating numerous prominent ecological patterns.
Scaling theories attempt to provide a general, predictive and synthetic framework for the structure and function of plants and animals that integrates across scales from cells to ecosystems. Scaling theories are grounded in the premise that general rules emerge from a focus on on how biological and ecological processes change as a function of scale – questions focused on how biological processes depend on body size, metabolism, area, and time are all fundamentally scaling problems.
The last few decades have seen intense research interest, debate, and other methodological and analytical activity with scaling approaches. There has been much work done to develop general scaling theories associated with biodiversity, ecosystem pattern and process, and the ramifications of metabolism. Much progress has been made in identifying patterns and revising and extending scaling theory in light of extensive new empirical data. Ecologists working across a range of scales have brought new information to bear and exciting advances have been made on many fronts.
Applications of scaling theory have been used to predict individual-level biological rates (e.g. primary production) and states (i.e. nutrient content), and the consequences of such phenomena at lower and higher levels of biological organization. The scope scaling approaches continue to expand and now encompasses a large array of biological phenomena – from the dynamics of cellular organelles to global patterns in biodiversity – and subdisciplines, including plant physiology, community ecology, and ecosystem science.
Our ESA symposium brings together a collection of ecologists working at the forefront of attempts to utilize integrative and synthetic approaches to modeling ecological patterns and processes. Research areas range from the adaptive nature of traits and biological networks to the structure and dynamics of plant and animal communities, scale dynamics of biodiversity and ecosystems to the role of body size in structuring food webs, to processes driving the flux of materials and energy at ecosystem scales. While the range of physical scales and taxa spanned by this group is considerable, all recognize and incorporate the central roles of scaling to their research programs.
Our goal is to consider the advances made in each area individually and also how the areas overlap in hopes that the insights gained from each respective scale can inform and enrich attempts at synthesis across scales.
Scaling Symposium Speakers
Metabolic Scaling: Pattern, Theory, and Future Van Savage, University of California, Los Angeles.
Temporal scaling of biodiversity: A missing component of building a predictive ecology Morgan Ernest, Biology, Utah State University
On the scaling of biodiversity distribution and fluctuation Pablo A. Marquet, Ecología, Pontificia Universidad Católica de Chile, Instituto de Ecologia y Biodiversidad, Santiago, Chile
Trophic interactions: Scaling approaches to developing a predictive theory for Ocean Sustainability in the face of climate change Julia L. Blanchard, Animal & Plant Sciences, University of Sheffield, Sheffield, United Kingdom
Scaling ecological data to reveal emergent properties of ecosystems Dennis Baldocchi, Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA
Using scaling theories to parameterize simulation models to forecast ecological environmental change. David Coomes, Department of Plant Sciences, University of Cambridge, United Kingdom
Is there a unified scaling theory for ecology and evolution? Karl J. Niklas, Department of Plant Biology, Cornell University, Ithaca, NY
The problem with biodversity science is that it has focused primarily on one metric – species richness. In the end, species richness, is just a number . . . That was the starting observation that lead to what we think is a new breakthrough in how we approach testing biodiversity theories. Lab graduate students Christine Lamanna, Benjamin Blonder and past lab post doc Cyrille Violle spearheaded an international effort to assess classic biodiversity theories from the perspective of functional ecology – in particular trait diversity. We just published the work in PNAS.
A new look at one of ecology’s unsolved puzzles — why biodiversity is higher in the tropics compared with colder regions — brought some unexpected revelations.
Here is the central thesis of the work- biodiversity theories have traditionally focused on species richness. The problem again is that species richness is just a number – it is dimensionally poor (number per unit area) and is difficult to connect to our theories which tend to be more closely tied to diversification rates, coexistence mechanisms, ecological interactions, and scaling which all tend to be measures that are more dimensionally rich (rates, change in numbers per unit time, per unit area, functional similarities and differences, phylogenetic similarities, time since last shared common ancestor, risk of extinction, propensity to diversify, risk of attack from biological enemies, etc. etc.). Focusing on number per unit area does not give us much information to test a broad suite of theories that focus on different mechanisms and can emphasize a different suite of processes in driving diversity gradients and the dynamics of biodiversity.
To quote a recent news story that featured the work. “Ever since the exploits of the European explorers and naturalists of the 17th and 18th centuries revealed a stunningly rich biodiversity in the tropics compared to the temperate regions of the world, biologists have wracked their brains over what causes this diversity. A research effort led by University of Arizona ecologists has now unearthed unexpected answers and helped found a new discipline — functional biogeography — in the process.”
“If we want to understand how ecosystems function, we have to go beyond cataloguing species and where they occur. As we want to be more predictive, especially with changes in climate, land use and human needs such as agriculture and sustainable forestry, we need to know how those systems work.” A functional or trait based approach allows us to link to a solid framework or organismal biology and geonomics in order to then build a more predictive ecology and more closely link our theories with evolutionary biology and biodiversity science.
“While the sheer number of species that live in rainforests and other tropical habitats is larger than farther north or south, it turns out that when taking into account their functions — in other words, what species do for a living — the temperate regions actually show a greater diversity of functions. It has long ago been proposed that the higher species diversity in the tropics could be explained by a larger number of habitats available for the organisms living there, while appealing, this hypothesis has not yet been tested in plants partly due to a lack of available data.”
A reverse latitudinal gradient in phenotypic function & diversity?
Surprisingly, we found the greatest diversity of functions in the temperate regions. See the movie to the side to help visualize these results.
Our work builds upon a unique and large global database compiled by an international group of researchers, the Botanical Information and Ecology Network, or BIEN. For this paper we analyzed data containing more than 20 million data entries of species occurrence and information about ecological functions for each species. We compared the diversity of functions carried out by species — as a proxy of the diversity of available habitats — in the tropics and in the temperate zones.
Our team was able to go back to several different biodiversity theories put forth as to why there are more species in the tropics, and evaluate them with regard to their assumptions on functional traits. In short our study assesses the biodiversity gradient in a completely different way. We looked at the diversity of functions — in other words, what plants do — and how organismal traits differ as we go from species-rich to species-poor environments. What we found was not what we were expecting. The results didn’t clearly match any biodiversity theory.
Our study revealed that, at least for the traits we focused on, the temperate latitudes trump the tropics with regard to the diversity of ecological functions, the question of why more species live in the tropics remains a mystery — for now. A fun way to visualize the result is this 3-D movie of functional trait space comparing tropical and temperate species.
It may be that a combination of different proposed theories that we already have can explain the latitudinal species diversity but it is clear that we still have a long way to go to fully understand how diversity changes across broad climatic gradients.
Big Data in Biology = Many advances in genomics but not enough in phenomics, macroecology & macroevolution
For this work the iPlant Collaborative, housed at the UA’s BIO5 Institute, has been critical for this research. The iPlant Collaborative’s goal is to connect to public datasets, manage and store their own data and experiments, access high-performance computing, and share results with colleagues. Our data intensive science could not have been done without the vision and support of iPlant. We used several big data approaches to assessing trait diversity and shifts in traits across gradients (phenomics) and applied them to trait data and species distribution data from all of North and South America, to make inferences about functional biodiversity from the tropics to the temperate zones. The tools and data infrastructure provided by iPlant helped us to quickly collect and analyze the data.
It wasn’t until recently that we have had access to all this data on not only where species occur and what they are, but also to their traits and the ecosystems they thrive in. With new tools to analyze new and rapidly growing large datasets, we can measure traits in large quantities — for example, wood density, seed size, how tall a plant is etc. All of these functional traits are ultimately connected to underlying genes, but in combination these trays collectively tell us about the diversity of organismal function and how an organism works and in what types of environments it can occur. The addition of large comparative trait data sources enables us to assess what processes shape the diversity of phenotypes across different environments.
“Don’t plant trees as trees warm the planet” – or how the selective use of science can advance your science agendaPosted: September 22, 2014
On saturday morning I woke up to read the following op ed piece in the New York Times entitled “To Save the Planet, Don’t Plant Trees” by Nadine Unger who is on the faculty at Yale University in the school of forestry. My first reaction was, really? don’t plant trees? Because of the seeming connection to a well respected school I was curious about scientific basis of this rather brash statement and I read Unger’s papers that appear to be central in the op ed piece.
I sent the article to my colleague here at the University of Arizona, Scott Saleska who quickly passed along several additional papers that helped get me up to speed on several dark corners of the science literature behind the piece. This led to some more back and forths about the science and a careful parsing through of Unger’s argument. Abigail Swan, from the University of Washington, in the department of Atmospheric Sciences joined in and also had important insights behind the science. In the span of a few hours emails which lead to more emails with colleagues were flying across the globe . . . it was encouraging to see a building consensus on this article.
I’ll be candid here . . . I think this is a reckless and borderline non-scientific piece – it is an opinion article that is not supported by the science. Unger selective picks some science findings, underweights a large number of studies, and greatly over extends some conclusions to extrapolate a rather non intuitive finding (dont plant trees!) to the globe. The dominant emphasis of this piece is that the UN effort on reforestry efforts is misplaced and wrong – this UN effort is focused on tropical forests but she goes on to argue that investing in forestry is a “bad bet”. The issue is that there is just no evidence for the statement “to save the planet, don’t plant trees” from the mountain of science that has been done on the role of trees and forests in regulating the earth’s climate system.
We wrote a rebuttal and submitted it to the New York Times. As we discuss below it is exactly in tropical reforestation where the biggest benefit of planting trees will be felt. There were many other issues that came up, accuracy of the science behind VOCs (the so called tree pollution), the surprising omission of the role of trees and forests in biodiversity preservation, the assumptions and accuracy of the models that Unger uses to accurately model the biosphere etc etc. However, we chose to write a simple letter and cut to the chase. In short, it is misleading to advance simplistic slogans for all forests that arise from a selective reading of the scientific literature.
Here is the letter that was sent to the New York Times early this morning
We disagree with Nadine Unger’s claim (Op-Ed, “To save the planet, don’t plant trees”) that “the science says that … climate change mitigation [through] forestry is high risk” and “a bad bet.” When it comes to preserving tropical forests — the main focus of the UN policy that Unger criticizes — the science says no such thing. In fact, science affirms the climate benefits of tropical forests, from the carbon stored in wood and soils to the cooling and rainfall recycling effects of water transpired though the leaves of trees.
Unger indicates in passing that tropical forests indeed cool climate, but then — inexplicably – argues that because complex effects in non-tropical forests can counteract the climate benefits of carbon storage, we should therefore undermine the UN program whose main effect will be to preserve tropical forests.
Slowing global warming is a sustainability challenge for our time. It is important that where the science supports action addressing this challenge – such as preserving tropical forests and their valuable biological diversity – we scientists report this accurately, rather than endorse simplistic slogans (like ‘don’t plant trees’) that could discourage positive steps by world leaders.
Scott R. Saleska, Associate Professor
Brian J. Enquist, Professor
Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
Abigail L. S. Swann, Assistant Professor, Department of Atmospheric Sciences and of Biology, University of Washington, Seattle, WA
After we submitted our piece it came to our attention that other scientists have also responded. Here is their letter that they have posted online. This group includes 6 members of the National Academy, 3 IPCC Lead Authors, and 1 IPCC Co-Chair
You can read their letter here http://news.mongabay.com/2014/0922-scientists-respond-to-dont-plant-trees-oped.html#Sl9yIhE7rgu9EhmI.99
Is ecology theory rich? Yes, but it is somewhat of an illusion . . . and much of the theory that we have really is not up for the challenge of guiding science in the era of “Big Data”. . . . that is the conclusion that we came up with after participating in one of the more stimulating working groups, spearheaded by Pablo Marquet, that I have participated in in quite some time. It was a fantastic meeting on a number of levels – it was a traveling workshop through Chile aimed at developing a novel approach forward.
One of the messages coming out of the meeting can be summed from this quote
“The grand aim of all science is to cover the greatest number of empirical facts by logical deduction from the smallest number of hypotheses or axioms.” (Albert Einstein)
Here is the problem, Ecologists are awash with data and we have a literal explosion of tools and new statistical approaches to seemingly find patterns in all this data. The issue is not so much ‘Big Data’ but rather knowing what to look for and understanding those patterns. The key struggle that we see ahead is to come up with simple, typically mathematical approaches.
To quote Pablo Marquet, “The complexity of the world is such that big data without big theory is scary, actually . . We need efficient theory, “to cope with complex and wicked environmental problems” and to develop a more predictive ecology.
So what is the solution? The group just published a paper with a proposed way forward for theory in Ecology. We argue for the need to refocus on ‘Efficient theory’. Efficient theory can addresses the challenges we face by building on robust foundations called first principles (basic, well-tested, core principles about the world), a small number of additional assumptions, and usually, though not always, mathematical descriptions of the world.
In this article, we argued for clarifying and expanding the role of theory in ecology to accelerate scientific progress, enhance our ability to address environmental challenges, and foster the development of synthesis and theory unification. Our primary goal is to identify characteristics of ecological theories that lead to more-rapid advancement. The development of more-efficient theories tend to make fewer, simpler, and more-fundamental assumptions and generate a greater number of testable predictions per free parameter than do less-efficient theories. The idea is that ecology will advance much faster if ecologists embrace efficient, approximate theories and improve on them through a process of successive refinements. The development of efficient theories, we contend, provides a robust epistemological framework to foster progress and synthesis in ecology.
Here is the abstract of the paper
“We argue for expanding the role of theory in ecology to accelerate scientific progress, enhance the ability to address environmental challenges, foster the development of synthesis and unification, and improve the design of experiments and large-scale environmental-monitoring programs. To achieve these goals, it is essential to foster the development of what we call efficient theories, which have several key attributes. Efficient theories are grounded in first principles, are usually expressed in the language of mathematics, make few assumptions and generate a large number of predictions per free parameter, are approximate, and entail predictions that provide well-understood standards for comparison with empirical data. We contend that the development and successive refinement of efficient theories provide a solid foundation for advancing environmental science in the era of big data.”
Here is a link to the paper
This past spring our lab set up a new NSF Macrosystems plot to add to our coordinated network of forest plots across latitude. You can read more about our NSF funded Macorystems project here. Benjamin Blonder in the lab wrote a nice blog post detailing our adventures and the various trials and tribulations with installing the plot which you can read here.
It was fun to introduce Professor Vigdis Vanvek who was visiting our lab on sabbatical from Norway to the thrills of installing a Gentraso as well as the impressive biodiversity as well as the fact that yes indeed we do have impressive forest and trees in southeastern Arizona . . .
Hypotheses that we are testing . . .
- a) Niche conservatism. Diversity may reflect variation in capacities to tolerate and adapt to extreme temperature conditions. Niche conservatism (Wiens et al. 2010) is being studied intensively using niche-based or climate-envelope models, phylogenetic analyses of trait evolution, and analyses of evolutionary constraints on composition of regional species pools.
- b) Kinetics. Temperature may affect diversity by its kinetic effect on the rates of biochemical, biological, and ecological processes (Gillooly et al. 2001). For organisms where ATP is generated as a result of heterotrophic respiration, the temperature dependence of most processes is approximately E ≈ 0.65 eV, equivalent to Q10 ≈ 2.5. MTE predicts that the rates of most organism-level processes and ecological interactions (and most evolutionary processes) exhibit similar temperature dependence.
- c) Productivity. Ultimately nearly all of the energy used by life on earth comes from the sun, is incorporated into organic molecules by photosynthesis, and then is respired to synthesize ATP to power biological processes. These processes are temperature-dependent with E ≈ 0.3 eV for photosynthesis and ≈ 0.65 eV for respiration (Allen et al. 2005). The effect of this potential energy on biodiversity is often couched in terms of productivity, because the presumed mechanism is that a higher rate of net primary production (NPP) per unit area of land, ocean, or fresh water can support more individuals which can be apportioned among more species with sufficiently high population densities to avoid stochastic extinction.
Our methods – Each of our NSF Macrosystems sites consists of a large 500m^2 plot. Here we sample plant, invertebrate and soil microbial diversity. Within each site our lab has set up five 0.1ha ‘Gentry’ plots. Each Gentry plot consists of 5 100x2m sample transects. Each 100m transect is separated by 8m so that the total external dimensions of the 0.1ha plot is 42m by 100m. These “Gentry” plots are used to sample the trees, saplings – marking and identifying to species all individuals >1 cm Diameter Breast Height. We also use the CTFS mapping protocol to measure the diameter at breast height of stems, including lianas and larger herbaceous plants. In addition, we will measure the basal stem diameter (at ground) height to map and measure additional stems that are greater than 1cm diameter at ground height. The addition of these smaller stems is allowing us to measure rates of turnover across a larger size range (small saplings and larger seedlings). All stems are tagged and given a unique tag number. Within each plot we will return to resurvey each 0.1ha plot in order to measure tree growth, mortality, and recruitment. All trees will have their diameter remeasured and any mortality recorded. Additionally, new recruits into the smallest size classes will be measured and entered into the dataset. In order to compare intra annual variation in tree growth across sites – we have also installed over 100 band dendrometers on a subset of trees within each Gentry plot. Dendrometer measures will help us assess errors of tree growth from dbh tape methods as well as provide a different measure of stem growth by which to compare.
Mt. Lemmon always is a wonderful and surprising place to visit and work – traveling from the lower elevations around Tucson the sights and plants of the Sonoran Desert soon are replaced with cool pine and fir forest. Being so close to the University of Arizona it is good to finally have a local forest field site. . . .
Must have SmartPhone Apps for the Field Ecologist and our contribution to to the smart phone app toolsPosted: August 22, 2014
The Bruno Lab has a nice series of recommendation for SmartPhone Apps for the Field Ecologist. Increasingly we find ourselves relying on our phone apps for not only data entry but also natural history, note taking, recording, remembering key must have/to do items etc. I was about to write a post about this but this lab link covers most of what the lab uses.
The potential power of smart phone apps came home to me after one of my graduate students Lindsey Sloat (seen dashing to the lab vehicle from one of her field sites in our above Lab Blog picture as well as conducting % cover plots in our RMBL research plots to the right) brought to our attention that the tedious measures of percent cover for grasses, shrub, soil, herbs etc. that we had been tallying by hand in a field book for several years could easily be entered and summed by a nice little app that enabled you to design a survey form and simply click on the box for each category to be counted. Since then there has been a proliferation of observation counting and recording apps out there.
Our contribution to the growing list of SmartPhone Apps
We (the BIEN working group) just released version 1.0 of Plant-O-Matic, a new smart phone app that will generate plant species lists for the plants that likely surround your present geographic location. It is free! What we are excited about is that this should work anywhere in North and South America (in the middle of the Amazon, on the top of a isolated mountain range, in the middle of the Yukon etc.) . This app helps answers the questions – What plants can I expect to see today? The BIEN Plant-O-Matic generates a list of plant species at 100 sq. km resolution for any location in the Americas. Pictures and information from the Missouri Botanical Garden help you identify and learn about each species. What is exciting is that this app will work for all plants (Embryophytes – bryophytes, ferns, gymnosperms, and angiosperms . . ).
Some details about our app: The BIEN Plant-O-Matic application generates a list of species in the user’s location at 100 sq. km resolution for any location in North and South America based on 3,585,449 standardized plant observations and geographic range models. With the app you can encounter ~100,000 Embryophyte species in the New World. The BIEN data represents a comprehensive effort to merge data from the world’s herbaria and ecological studies. Some geographic areas are better represented than others. While efforts were made to remove them, known issues include presence of cultivated species and over-prediction of some species geographic ranges. The application is intended as a general reference to discover the botanical diversity that likely exists around you; all data is provided “as is,” BIEN, Ocotea Technologies and their affiliates take no responsibility for the accuracy of the output. Additional details regarding the data, analysis, and other botanical tools can be found at http://bien.nceas.ucsb.edu/bien/.
As we have been developing the app it was clear that we had a long laundry list of new features and options to include in the app. In fact there were so many that it was clear we had to start bare bones and slowly add new features. So, this is the baseline version 1.0 of Plant-O-Matic. Look for updates soon with more information, a better interface, and more options to learn and discover all the plants that are found around you. We would be keen for any advice and suggestions for how to improve the app which you can submit directly to us via info[at]ocoteatech.com .
Updates to this post – Since posting several have contacted us with questions (see for example below)
Note for iPad users – Plant O Matic will work on the iPad but it is customized for the iPhone. This means that the images that are brought up on the image carousel will look low resolution – however please know you can touch or click the image and the high resolution image will then down load for you. You can two finger enlarge the image even more.
Note for Android users – We do hope to release an Android version of Plant O Matic but this will likely not be for several months. Keep checking back and thank you for your input and interest.
A big and hearty congratulations to Sean Michaletz. He was just announced the winner of the 2013 Plant, Cell and Environment Postdoctoral Award for his presentation “Intra- and interspecific tree growth rates across a broad climate gradient: Toward a general metabolic scaling model linking climate, functional traits, and individual plant growth“ at the Ecological Society of America meeting in Minneapolis. This is the ESA Physiological Ecology award for the best oral presentation given by a postdoc at the 2013 meetings.
You can read the winning talk abstract here.