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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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

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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