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
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
UCOct.
San
Richard C. Atkinson Hall Dedication
28,Diego
2005
UC Irvine
www.calit2.net
Preparing for an World in Which
Distance Has Been Eliminated…
Calit2--An Integrated Approach
the Future of the Internet
220 UC San Diego & UC Irvine Faculty
Working in Multidisciplinary Teams
With Students, Industry, and the Community
Creating Cross-Disciplinary Teams
for Sensing the Environement
www.calit2.net
NASA’s Earth Science Enterprise
Fundamental Science Questions
How Is The Earth Changing And
What Are The Consequences Of
Life On Earth?
• 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?
I was Chair of NASA’s Earth System Science &
Applications Advisory Committee (ESSAAC)
NASA Earth Science Research Satellites
Jason
Landsat 7
Aqua
SORCE
SAGE III
QuikScat
EO-1
SeaWiFS
ICESat
TRMM
SeaWinds
ACRIMSAT
TOMS-EP
ERBS
GRACE
Terra
UARS
TOPEX/Poseidon
Visionof
for
Creating
an Integrated
Interactive
Components
a Future
Global
System for Earth
Observation
(Sensor
Information System
forWeb)
Earth Exploration
Earth System Science
Technology Emphasis Areas
Earth System Science in the Future Will Leverage
Three Ongoing Technology Revolutions:
Geospatial
Computing
Communications
...To Enable Timely and Affordable Delivery of
Earth Science Data and Information to Users
How to Integrate Biodiversity Knowledge?
Localities of Plant Specimens in Different Herbaria
UADY (University de Yucatan)
TEX (Universidad de Texas en Austin)
ARIZ (University de Arizona)
CIDIIR (Centro de Investigaciones
Científicas de Durango)
Source: Jorge Soberon
First Create Digital Library of Physical Specimens
XAL (Instituto de Ecología de Xalapa)
CICY (Centro de Investigaciones
Científicas de Yucatan)
CAS (California Academy of Sciences)
MEXU (Universidad Nacional Autónoma
de México)
Source: Jorge Soberon
Then Federate the Data together...
The Virtual Herbarium of Mexico
700,000 Registers from 25 Herbaria
In Mexico and the United States.
Source: Jorge Soberon
Evolution is the Principle of Biological Systems:
Most of Evolutionary Time Was in the Microbial World
You
Are
Here
Much of Genome
Work Has
Occurred in
Animals
Source: Carl Woese, et al
Looking Back Nearly 4 Billion Years
In the Evolution of Microbe Genomics
Science Falkowski and Vargas 304 (5667): 58
The Sargasso Sea Experiment
The Power of Environmental Metagenomics
•
•
•
•
MODIS-Aqua satellite image of
ocean chlorophyll in the Sargasso
Sea grid about the BATS site from
22 February 2003
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
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 Project
Measuring 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
CAMERA will include
All Moore Marine Microbial Genomes
www.moore.org/microgenome/trees_main.asp
Moore Microbial Genome Sequencing Project
Selected Microbes Throughout the World’s Oceans
www.moore.org/microgenome/worldmap.asp
Coupling Ocean Current Models
to Remote Data Sources Including Biology
NASA MODIS Mean Primary Productivity
for April 2001 in California Current System
Regional Ocean Modeling System (ROMS)
http://ourocean.jpl.nasa.gov/
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
Central
Lander
MARS Installation
Oct 2005 -Jan 2006
Source:
Jim
Bellingham,
MBARI
Tele-Operated
Crawlers
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 Instruments
in the Santa Margarita Ecological Reserve
Source, Dan Cayan, UCSD SIO
Grand Challenge: A Total Knowledge Integration System
Pilot
Components
forProject
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
Antelope
SRB
Web Services
Frank Vernon, SIO; Tony Fountain, Ilkay Altintas, SDSC
Kepler
Groups are Forming to Monitor
Remote Environments in Real Time
Workshop
29th to 31st
March 2006
Townsville,
Australia
Steering Committee
-Peter Arzberger, UCSD, USA
-David Hamiltion, University of Waikato,
New Zealand
-Tim Kratz, University of Wisconsin, USA
-Fang-Pang Lin, NCHC, Taiwan
Programs
-Australia
-Canada
-China
-Finland
-Florida
-New Zealand
-Israel
-South Korea
-Taiwan
-United Kingdom
-Wisconsin
First meeting:
San Diego
March 7-9, 2005
Source: T. Kratz
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?
Remote Observation of Episodic Events
in Water-Based Ecological Systems
Typhoon
20
18
Photo by Peter Arzberger, October 2004
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18
16
14
12
10
8
6
14
4
2
12
22-Aug
0
23-Aug
24-Aug
25-Aug
26-Aug
27-Aug
28-Aug
Date
Part of a growing global lake observatory network http://lakemetabolism.org
Source: Tim Kratz
Supported by Moore Foundation
(mm per 5 minute interval)
0.5 meters
1 meter
1.5 meters
2 meters
2.5 meters
3 meters
Precipitation
20
Precipitation
Used by NSF Director Feb 2005
Water Temperature (°C)
22
Access can be
difficult
during2004
the
Yuan Yang Lake, Taiwan
– August
most interesting times
Surface
Scalable Instrumentation and
Cyberfrastructure is Critical
Source: Tim Kratz
We Can Do This Scale Now
http://lakemetabolism.org
Long Term Goal:
A Global Real-Time Network of Environmental Sensors
Source: Tim Kratz
Calit2, SDSC, and SIO are Building
Environmental Observatory Control Rooms