Toward a Global Monitoring of Environmental Biodiversity
Invited Talk
Undergraduate Course in IR/PS
University of California, San Diego
March 8, 2006
Dr. Larry Smarr
Director, California Institute for Telecommunications and Information Technologies
Harry E. Gruber Professor,
Dept. of Computer Science and Engineering
Jacobs School of Engineering, UCSD
UC San DiegoRichard C. Atkinson Hall Dedication Oct. 28, 2005
Two New Calit2 Buildings Will Provide Major New Laboratories to Their Campuses
• New Laboratory Facilities– Nanotech, BioMEMS, Chips, Radio, Photonics,
Grid, Data, Applications– Virtual Reality, Digital Cinema, HDTV, Synthesis
• Over 1000 Researchers in Two Buildings– Linked via Dedicated Optical Networks– International Conferences and Testbeds
UC Irvine
www.calit2.net
Preparing for an World in Which Distance Has Been Eliminated…
Calit2--An Integrated Approach the Future of the Internet
www.calit2.net
220 UC San Diego & UC Irvine FacultyWorking in Multidisciplinary Teams
With Students, Industry, and the Community
Creating Cross-Disciplinary Teams for Sensing the Environement
NASA’s Earth Science Enterprise Fundamental Science Questions
• How is the Global Earth System Changing?• What are the Primary Forcings of the Earth
System?• How Does the Earth System Respond to Natural
and Human-Induced Changes?• What are the Consequences of Changes in the
Earth System for Human Civilization?• How Well Can We Predict Future Changes in the
Earth System?
How Is The Earth Changing And What Are The Consequences Of
Life On Earth?
I was Chair of NASA’s Earth System Science & Applications Advisory Committee (ESSAAC)
ERBS
Terra
Aqua
GRACE
QuikScatSAGE III
SeaWinds
TRMM
TOMS-EP
UARS
Jason Landsat 7
SORCE
ACRIMSAT
EO-1
TOPEX/Poseidon
SeaWiFS
ICESat
NASA Earth Science Research Satellites
Components of a Future Global System for Earth Observation(Sensor Web)
Vision for Creating an Integrated InteractiveInformation System for Earth Exploration
Geospatial
...To Enable Timely and Affordable Delivery of Earth Science Data and Information to Users
Computing
Earth System Science in the Future Will Leverage Three Ongoing Technology Revolutions:
Earth System Science Technology Emphasis Areas
Communications
TEX (Universidad de Texas en Austin)UADY (University de Yucatan)
ARIZ (University de Arizona)CIDIIR (Centro de Investigaciones
Científicas de Durango)
Source: Jorge Soberon
How to Integrate Biodiversity Knowledge?Localities of Plant Specimens in Different Herbaria
XAL (Instituto de Ecología de Xalapa)CAS (California Academy of Sciences)
MEXU (Universidad Nacional Autónomade México)
CICY (Centro de Investigaciones Científicas de Yucatan)
Source: Jorge Soberon
First Create Digital Library of Physical Specimens
The Virtual Herbarium of Mexico700,000 Registers from 25 HerbariaIn Mexico and the United States.
Source: Jorge Soberon
Then Federate the Data together...
Evolution is the Principle of Biological Systems:Most of Evolutionary Time Was in the Microbial World
You Are
Here
Source: Carl Woese, et al
Much of Genome Work Has
Occurred in Animals
Looking Back Nearly 4 Billion YearsIn the Evolution of Microbe Genomics
Science Falkowski and Vargas 304 (5667): 58
The Sargasso Sea Experiment The Power of Environmental Metagenomics
• Yielded a Total of Over 1 billion Base Pairs of Non-Redundant Sequence
• Displayed the Gene Content, Diversity, & Relative Abundance of the Organisms
• Sequences from at Least 1800 Genomic Species, including 148 Previously Unknown
• Identified over 1.2 Million Unknown Genes
MODIS-Aqua satellite image of ocean chlorophyll in the Sargasso Sea grid about the BATS site from
22 February 2003
J. Craig Venter, et al.
Science 2 April 2004:
Vol. 304. pp. 66 - 74
PI Larry Smarr
First Implementation of the CAMERA Complex
Compute Database &Storage
Marine Genome Sequencing ProjectMeasuring the Genetic Diversity of Ocean Microbes
CAMERA will include All Sorcerer II Metagenomic Data
Moore Foundation Funded the Venter Institute to Provide the Full Genome Sequence of 150 Marine Microbes
www.moore.org/microgenome/trees_main.asp
CAMERA will include All Moore Marine Microbial Genomes
Moore Microbial Genome Sequencing ProjectSelected Microbes Throughout the World’s Oceans
www.moore.org/microgenome/worldmap.asp
Coupling Ocean Current Models to Remote Data Sources Including Biology
Regional Ocean Modeling System (ROMS) http://ourocean.jpl.nasa.gov/
NASA MODIS Mean Primary Productivity for April 2001 in California Current System
Goal – From Expedition to Cable Observatories with Streaming HDTV Robotic Cameras
Scenes from The Aliens of the Deep, Directed by James Cameron &
Steven Quale
NSF’s Ocean Observatories Initiative (OOI)Envisions Global, Regional, and Coastal Scales
LEO15 Inset Courtesy of Rutgers University, Institute of Marine and Coastal Sciences
High Definition Video - 2.5 km Below the Ocean Surface
Monterey Accelerated Research System (MARS) Cable Observatory Testbed
Tele-Operated Crawlers
Central Lander
MARS Installation Oct 2005 -Jan 2006
Source: Jim
Bellingham, MBARI
A Near Future Metagenomics Fiber Optic Cable Observatory
Source John Delaney, UWash
ROADnet and HiSeasNet are Prototypes of the Future of In Situ Earth Observing Systems
http://roadnet.ucsd.edu
Environmental SensorNets--Water and Climate Instrumentsin the Santa Margarita Ecological Reserve
Source, Dan Cayan, UCSD SIO
Pilot Project ComponentsPilot Project Components
Grand Challenge: A Total Knowledge Integration System for the Coastal Zone
• Moorings• Ships• Autonomous Vehicles • Satellite Remote Sensing• Drifters• Long Range HF Radar • Near-Shore Waves/Currents (CDIP)• COAMPS Wind Model• Nested ROMS Models• Data Assimilation and Modeling• Data Systems
www.sccoos.org/
www.cocmp.org
ROADNet Architecture: SensorNets, Storage Research Broker, Web Services, Work Flow
KeplerWeb ServicesSRBAntelope
Frank Vernon, SIO; Tony Fountain, Ilkay Altintas, SDSC
Groups are Forming to Monitor Remote Environments in Real Time
Workshop 29th to 31st March 2006 Townsville, Australia
Programs-Australia-Canada-China-Finland-Florida-New Zealand-Israel-South Korea-Taiwan-United Kingdom-Wisconsin
First meeting:San DiegoMarch 7-9, 2005
Source: T. Kratz
Steering Committee-Peter Arzberger, UCSD, USA-David Hamiltion, University of Waikato, New Zealand-Tim Kratz, University of Wisconsin, USA-Fang-Pang Lin, NCHC, Taiwan
What is the “Global Lake Ecological Observatory Network?”
• A Grassroots Network of:– People: Lake Scientists, Engineers,
Information Technology Experts– Institutions: Universities, National
Laboratories, Agencies– Programs: PRAGMA, AS-Forest
Biogeochemistry,US-LTER, TERN, KING, EcoGrid, etc.
– Instruments – Data
• Linked by a Common Purpose and Cyberinfrastructure
• With a Goal of Understanding Lake Dynamics at Local, Regional, Continental, and Global Scales
Source: T. Kratz
Example Science Questions for GLEON
• How do Nutrient Loading, Hydrology, Geologic Setting, and Climate Regime Influence the Metabolic Balance in Lakes?
• How do Physical, Chemical, and Biological Processes Interact to Control Inorganic and Organic Carbon Fluxes in Lakes and Does This Interaction Vary With Scale?
• What Roles do Large-Scale Disturbances (e.g. Typhoons and Drought) Play in Structuring Lake Biological Communities and Their Dynamics?
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Precipitation
Typhoon
Yuan Yang Lake, Taiwan – August 2004
Part of a growing global lake observatory network - http://lakemetabolism.org
Access can be difficult during the most interesting times
Photo by Peter Arzberger, October 2004
Us
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Source: Tim Kratz
Remote Observation of Episodic Events in Water-Based Ecological Systems
Supported by Moore Foundation
We Can Do This Scale Now
http://lakemetabolism.org
Source: Tim Kratz
Scalable Instrumentation and Cyberfrastructure is Critical
Source: Tim Kratz
Long Term Goal:A Global Real-Time Network of Environmental Sensors
Calit2, SDSC, and SIO are Building Environmental Observatory Control Rooms