Introduction to Jupyter notebooks and quick dive into Python

Posted on November 28, 2016 by Halley Froehlich

Presenter: Julien Brun

Jupyter notebooks are a great way to share your data analysis and promote reproducible science. These interactive notebooks mix executable computer code (e.g. Python, R, Julia, Bash, …) with rich text and data visualizations. Have a look here for some examples: https://nbviewer.jupyter.org. We will use this tool to do a quick dive into Python with specific tips for R users.

Note that the hands-on participation is space-limited and you need to register here. However, everybody is welcome to follow the session in person or remotely. The hands-on participants will need to bring their laptop to connect to NCEAS’ server, but no specific installation is required.

Plant Community Responses to Global Change Drivers

Posted on November 28, 2016 by Halley Froehlich

Global change will alter resources, which are predicted to change the composition and functioning of plant communities. Here, I present the results of several projects studying plant community changes in response to resource manipulations. First, I present data from an experiment at Konza Prairie Biological Station in Manhattan Kansas. In this experiment, nutrient additions (nitrogen and phosphorus) turned the tallgrass prairie from being dominate by C4 grasses to C3 forbs. Next, I detail plant community responses to resource manipulations across ~100 experiments world-wide. This data synthesis found that when 5 factors are simultaneously manipulated, there are drastic changes in the plant community. Additionally, the greater number of factors that are manipulated, the greater the change in productivity. Lastly, I review my current postdoctoral work, focused on developing new ways to study patterns of community change using rank abundance curves.

Photo of the phosphorus plots experiment at Konza Prairie Biological Station. Photo Credit: Melinda Smith

Carbon Neutrality at University California: The TomKat Project

Posted on November 9, 2016 by Halley Froehlich

Abstract

In 2013, University of California President Janet Napolitano announced the UC Carbon Neutrality Initiative, which declares that all ten campuses in the University of California will have zero net emissions by the year 2025. Through a generous donation from the TomKat Foundation and supplemental funding from the University of California Office of the President, two groups of researchers have assembled to help address different facets of this multidimensional initiative. These two teams of the TomKat Project are hosted by the National Center for Ecological Analysis and Synthesis and supported by the Institute for Energy Efficiency at UCSB.

The Exit Strategies for Natural Gas working group is focusing on the challenge of eliminating natural gas emissions from the ten UC campuses and their medical centers. This is made difficult by the lock-in situation that exists at six campuses which rely on cogeneration power plants for heating and power. The Net-Zero Comm Strategy working group will work to develop and test best communication techniques for the University of California to achieve zero net emissions by 2025. This process will involve performing audience research on key stakeholders at the University of California, testing messages, and analyzing barriers to gaining support for the Carbon Neutrality Initiative.

Speakers

Celine Mol is an undergraduate student at UC Santa Barbara, where she is graduating this coming June with a Bachelor’s degree in Statistics and Applied Probability. In her future, Celine would like to be able to use her strengths in data science to find solutions that demand a more sustainable future. Through the Net-Zero Comm Strategy Working Group, Celine is excited to focus on approaches to leveraging influencers and developing outreach and engagement strategies to implement a successful carbon neutrality model at the UC.

Charlie Diamond is a second year MESM student at the Bren School of Environmental Science & Management. He has an undergraduate degree in environmental economics, and is specializing in water resources management at the Bren School. Charlie is interested in water and climate policy in California, and feels lucky to be part of an exciting research effort to evaluate decarbonization strategies at the University of California as a TomKat intern.

Evan Ritzinger is serving as an Intern for the TomKat Project on strategies for natural gas removal. He is a Master’s candidate of Environmental Science and Management at the Bren School of Environmental Science & Management at UC Santa Barbara, where he is pursuing a dual specialization in Conservation Planning and Energy & Climate. His research interests include energy efficiency and climate change mitigation. Previously, Evan worked for roughly two years as a Home Energy Advisor for a Boston based energy efficiency firm, where he was certified as a Building Analyst under the Building Performance Institute and performed hundreds of energy audits. Evan received his B.A. in Environmental Science with a minor in Economics from Boston University.

Jay McConagha is a second year MESM student at the Bren School of Environmental Science & Management. He is specializing in Energy & Climate while completing a focus in Strategic Environmental Communication & Media. As an intern with the Net-Zero Comm Strategy working group, Jay is interested in identifying and overcoming barriers to the goals of the Carbon Neutrality Initiative, and fostering support through strategic communication.

TomKat Foundation
Established in 2009 by Tom Steyer and Kathryn Taylor, the TomKat Foundation partners with innovative organizations that envision a world with climate stability, a healthy and just food system, and broad prosperity. The Foundation embraces the inherent interconnectedness of these complex systems. Working at every level, the TomKat Foundation is committed to supporting organizations and initiatives across the country that will take bold action on climate change.

Species interactions as biotic filters of global change [Wed. Oct. 12]

Posted on October 7, 2016 by Rachael Blake

The study of species interactions has greatly improved our appreciation of the importance of network structure for ecological community stability, sensitivity to invasion, and extinction. Because species interactions reflect past evolutionary constraints and niche partitioning within a particular local context, they constitute the underlying fabric of ecosystem dynamics, driving biomass and body size distributions, and ecosystem level processes. Here I propose that beyond being a simple witness of global change, species interactions can actually mediate their effects on population and ecosystem dynamics either locally via bottom-up or top-down mechanisms or regionally via spatial cascade processes. I will present case studies for each scenario and conclude with a discussion of future perspectives and challenges for the use of ecological networks in conservation biology.

Eric Harvey, PhD

Department of Evolutionary Biology and Environmental Studies

University of Zurich

Zurich, Switzerland

http://ericharvey.weebly.com/

Interactive Tradeoffs to Support Anticipatory Marine Spatial Planning [Wed. Sept.14]

Posted on September 12, 2016 by Halley Froehlich

Human use of the oceans is increasingly in conflict with conservation of endangered species. Evaluation of environmental impacts have historically been post hoc; the time and place of human activity is often already proposed before assessment. I describe anticipatory spatial decision support frameworks that highlight tradeoffs between industry and conservation with interactively synchronized map and tradeoff plots for two spatially distinct problems: siting for offshore wind energy development (OWED) and routing for ships to avoid striking whales.

Offshore wind energy development suffers from a lengthy environmental compliance process, estimated to incur a 7 to 10 year permitting timeline in the US. To responsibly and expeditiously evaluate environmental impacts we differentially assess sensitivity of wildlife above the water line in space, and below the water line in time. During long-term OWED operation, birds can collide and be displaced by active turbines. During episodic pre-operation phases, cetaceans are most heavily impacted acoustically by seismic airgun surveys and pile driving. The framework highlights sites in space that are most profitable and least sensitive to birds. For a given site, pre-operation activities are advised by cetacean sensitivity across months of the year that minimize impacts on migratory cetaceans, particularly those of highest conservation concern such as the North Atlantic right whale (Eubalaena Glacialis) in the case of the US Mid-Atlantic study area.

For routing ships to avoid whale strikes, British Columbia is evaluated in light of potential new oil tanker traffic to Port Kitimat where an oil pipeline terminal is under consideration. Marine mammal species distributions are aggregated to a single map layer, weighted by species conservation concern. This map layer of risk to species acts as the resistance surface by which least-cost routing is implemented. Transformations are applied to this surface before the routing algorithm for providing a series of routes offering a range of tradeoffs between conservation and industry. Preemptive avoidance of whale hotspots by ships could theoretically become as commonplace in the oceans as traffic avoidance by cars with Google Maps.
The web-based interfaces are built using the open-source, cross-platform R package shiny. Future developments and broader applications will be discussed.

Ben Best is an environmental data scientist with a strong background in marine spatial ecology. He offers consulting services, current clients of which include the Ocean Health Index and Marine Biodiversity Observation Network. He has lectured at UCSB’s Bren School of Environmental Science & Management for several courses (GIS, Advanced GIS, Landscape Ecology, Environmental Informatics) as well as Duke University’s Nicholas School of the Environment (Marine GIS). He was previously employed as a senior analyst for the Ocean Health Index and research associate for development of the OBIS-SEAMAP marine animal observation geoportal. He recently completed a PhD at Duke University’s Nicholas School from the Marine Geospatial Ecology Lab and obtained an MS in Environmental Sciences from Duke, and from UCSB a BS in Aquatic Biology and BA in Geography.

Ben Best, Ph.D.
bbest@nceas.ucsb.edu

Greening Games [Wed. Sept. 7]

Posted on August 30, 2016 by Halley Froehlich

This talk will examine the potential affinities between ecology and environmental science and digital interactive games. Although video games and the platforms that run them seem woefully remote from the concerns of the outside world, contemporary games may offer quantitatively and qualitatively distinctive opportunities for the representation of pressing environmental problems. Touching on both commercial titles like Spore and No Man’s Sky and academically developed games like Future Delta and AirQuest, I will argue that games not only meld the computational advantages of programming-driven processes with the aesthetic range of literature and cinema, but more importantly render environmental outcomes and ethics into powerfully playable scenarios.

Professor Chang is an Assistant Professor in the Department of Film and Media Studies at UC Santa Barbara (Ph.D. Rhetoric, UC Berkeley). With a multidisciplinary background in biology, literature, and film, she combines ecocritical theory with the analysis of contemporary media. Her current project, Playing Nature, offers an ecological perspective on computer and video games. She also maintains the Growing Games blog, a resource for scholars in game and ecomedia studies and the environmental humanities.

Alenda Y. Chang
Assistant Professor
Department of Film and Media Studies
2018 Social Sciences and Media Studies Building
University of California, Santa Barbara
Santa Barbara, CA 93106-4010

This, That, and The Other: Three Remarks on the Sociology of Creativity [Wed. July 20]

Posted on July 14, 2016 by Rachael Blake

This talk will review some of my current research on creativity in science and art:

1. Sociometric sensors promise to measure social interactions quantitatively, precisely, and unobtrusively. I’ll discuss a few findings from a pilot study of small group collaborations at two synthesis centers.

2. Path-breaking groups of artists and scientists that launch major artistic and intellectual movements share much in common, but also differ markedly along some social dimensions due to key differences between the fields of art and science. I’ll discuss some of these similarities and differences in relation to the specific character of these fields.

3. How theory groups die: I’ll discuss the social forces that cause the small groups that create new scientific paradigms to disintegrate, socially and creatively.

Dr. John N. Parker
Barrett, The Honors College
Arizona State University
john.parker at asu.edu

Fostering Sci. Community at NCEAS: Welcome Site for Newcomers [Wed. July 13]

Posted on July 8, 2016 by Halley Froehlich

NCEAS is a central hub for a diverse array of scientists and research. New researchers, including visiting and early career researchers (ECRs), are constantly coming in and out at various frequencies. However, larger cohorts of scientists stationed at NCEAS are no longer entering at one time, making it more difficult to track the exciting research and possible collaborations within the center. As part of addressing this new dynamic, the resident ECRs are proposing a simple, advice-based website that provides basic and clear information concerning everything from housing to setting up access to the NCEAS servers. It simply provides the fundamentals of what an incoming scientist will need/can do before moving to Santa Barbara and within the first couple weeks here. The ECRs will maintain most of the site, allowing us to modify the information quickly when new issues or ideas arise. The beta-version of the site will be discussed and feedback is most welcome!

Looking forward to the discussion!

Halley E. Froehlich
Rachael Blake
Jamie Afflerbach
Casey O’Hara
Heather Soyka
Colette Ward
Claire Runge

Catering for wildlife in fire-prone Australian mallee habitats: it’s not rocket science, it’s more complex than that! [Wed. July 6]

Posted on July 1, 2016 by Rachael Blake

Inappropriate fire regimes are recognized as a key threatening process to bird conservation globally, but particularly in Australia. Fire management often aims to maintain a “mosaic” of patches of differing fire history (pyrodiversity); assuming this will cater for the greatest variety of species. We tested this assumption across a 104,000 km² area of the Murray Mallee region of southern Australia. We compared avian diversity in 28 ‘whole’ landscapes, representing different fire-driven mosaics.

Using a novel technique to age and map vegetation we demonstrated that fire influences mallee vegetation for over a century, particularly key habitat resources (e.g. tree hollows). We found little evidence that bird diversity was related to the diversity of fire age classes in a landscape. Similarly, there was little evidence of the importance of pyrodiversity for individual species. Instead, a key driver for all groups was the spatial extent of ecologically important fire age classes; in particular, the spatial extent of long-unburned mallee vegetation.

We used models of species distributions to evaluate the consequences for threatened bird species of alternative management scenarios for fire for the next twenty years. We evaluated the likely effect of planned burning programs that burnt 1%, 3% or 5% of public land annually. The outcomes of this work have provided an assessment of the relative risk of extinction for these species. This research has transformed understanding of how fire affects these threatened species in the region and has been embraced by fire managers and contributed to significant change in fire management policy.

Prof. Mike Clarke
Department of Ecology, Environment and Evolution
La Trobe University, Australia
http://www.latrobe.edu.au/ecology-environment-evolution/research/specialisations/fire-ecology

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