New approaches to the study of biological diversity

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Name Registration One Less Impediment to
Taxonomy Jim Woolley Texas AM
University Revolutionising taxonomy through an
open-access web-register for animal names and
descriptions ESA Program Symposium December, 2005
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A Renaissance in Systematics

• Collecting
• Preparation of specimens
• Study of specimens
• Revisions, monographs
• Access to literature
• New Technologies
  
  
  
  

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New Technologies for Taxonomists

• Digital technologies have changed all the rules
• Taxonomic collections, literature, expertise,
  digital libraries, virtual monographs should
  become a distributed, virtual research tool and
  education resource.

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The New Taxonomy

• Web-based - Web provides a single, global point
  of access
• Distributed - eg gt 350 web sites for Lepidoptera
• Authoritative - need Electronic Catalog of Life
• Accessible to multiple audiences
• Relevant to societal concerns - natural resource
  management, invasive species, agriculture,
  medicine etc.
• Taxonomic publications should not be end points,
  but version control devices

(thanks to Malcolm Scoble, Natural History Museum)
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Impediments to The New Taxonomy

• Lack of funding
• Funding for taxonomy is insufficient
• Most funding for systematics is devoted to
  constructing molecular phylogenies, not taxonomy
• Not enough taxonomists
• Taxonomy is too difficult to learn and to
  practice
• Requires years to accumulate literature,
  specimens etc.
• Critical resources are scattered and available to
  only a few workers
• Literature
• Museum specimens
• There are few centralized sources of information

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NSF has recognized the funding issues

• Planetary Biodiversity Inventory (PBI)
• Global assaults on taxonomy of major groups
• RevSys - Revisionary Syntheses in Systematics
• Species-level treatments
• Develop new methodologies for revisionary work
• PEET - Partnerships for Enhanced expertise in
  Taxonomy
• Long-term monographic research
• Major training component

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ZOOBANK

• ZOOBANK will go a long way towards providing
  centralized sources of information
• We may quibble about the details and plan for
  implementation
• But this is really essential for progress

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The Atkins Report

• Daniel Atkins, University of Michigan
• 8 other authors from academia and industry

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Atkins Report

• The Panels overarching finding is that a new
  age has dawned in scientific and engineering
  research,
• pushed by continuing progress in computing,
  information, and communication technology,
• and pulled by expanding complexity, scope and
  scale of todays challenges

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Atkins Report

• The capacity of this technology has crossed
  thresholds that now make possible a comprehensive
  cyberinfrastructure
• on which to build new types of scientific and
  engineering knowledge environments and
  organizations,
• and to pursue research in new ways and with
  increased efficiency

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Atkins Report

• use cyberinfrastructure to build more ubiquitous,
  comprehensive digital environments
• interactive and functionally complete for
  research communities in terms of people, data,
  information, tools, and instruments
• operate at unprecedented levels of computational,
  storage, and data transfer capacity

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Cyberinfrastructure will include

• grids of computational centers, some with
  computing power second to none
• comprehensive libraries of digital objects
  including programs and literature
• multidisciplinary, well-curated, federated
  collections of scientific data
• thousands of on-line instruments and sensor
  arrays,
• convenient software toolkits for resource,
  discovery, modeling and interactive visualization
• ability to collaborate with physically
  distributed teams of people using all of these
  capabilities

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Atkins Report

• many contemporary projects require effective
  federations
• distributed resources (data and facilities)
• distributed, multidisciplinary expertise
• (harvest of legacy data)

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Virtual Science Communities

• National Ecological Observatory Network (NEON)
• National Virtual Observatory (NVO)
• Space Physics and Aeronomy Research Collaboratory
  (SPARC)
• Grid Physics Network (GriPhyN)
• Biomedical Informatics Research Network (BIRN)
• National Science Digital Library (NDSL)

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Recent Workshops Sponsored by NSF

• Workshop to Produce Decadal Vision for Taxonomy
  and Natural History Collections, Gainesville,
  November 2003
• Development of a National Systematics
  Infrastructure A Virtual Instrument for the 21st
  Century, New York Botanical Garden, December 2003
• Workshop to Establish a Comprehensive Database
  for Plant Systematics, Gainesville, December 2003
• Biological Image Database Workshop, Tallahassee,
  Florida, September 2004

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A BIODIVERSITY OBSERVATORY LINNÉ LEGACY
INFRASTRUCTURE NETWORK FOR NATURAL ENVIRONMENTS
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Each collection or taxonomic research facility is
potentially a node of a NATIONAL CYBERLABORATORY

• Each node will contribute its own particular
  strengths to the network
• (e.g., taxonomic or geographic uniqueness, unique
  instrumentation)
• The resources of each node will be available to
  all nodes
• (e.g., specimens, images, literature, DNA data)

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Implementation of LINNE will

• Modernize the national infrastructure for
  taxonomic research
• high resolution 2D and 3D surface and internal
  scanning using computer tomography
• Remote-controlled, digital microscopy
• Comprehensive digital libraries
• Modernize collection facilities
• Provide comprehensive access to taxonomic and
  collections information, worldwide
• Provide new tools for education and outreach

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Virtual Research Platform

• Remove the taxonomic impediment
• See across historical and geological time,
  continents and seas, species and clades,
  ontogenetic paths ecosystems.

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The Big Questions

• What are earths species, and how do they vary?
• How are species distributed in geographical and
  ecological space?
• What is the history of life on Earth, and how are
  species interrelated?
• How has biological diversity changed through
  space and time?
• What is the history of character transformations?
• What factors lead to speciation, dispersal and
  extinction?

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Is the vision impossibly grand?

• Virtually all of the necessary technology is is
  already in place or will be in the next few years
• Many national and international activities are
  already underway

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Key Activities Related to Collections and
Bioinformatics

• SEEK
• NESCent
• CIPRES
• Species Analyst
• MaNIS
• HerpNET
• FishNetII
• ORNIS
• ENHSIN
• BioCASE
• BioCISE
• MaPSTEDI

• DiGIR
• Specify
• BioGeoMancer
• Species2000
• ITIS
• TDWG
• OBIS
• uBIO
• IPNI
• DRSC
• Index Herbariorum

• PBI
• ERIN
• CONABIO
• CBIN
• CHM
• WDC
• IABIN
• PBIF
• CBOL
• MorphBank
• MorphoBank
• Digimorph
• and ???

• Zoobank
• NBII
• GBIF
• Synthesys
• EBNI
• CHRONOS
• NEON
• NSCA

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• Linking databases, informatics products and
  analytical tools for data sharing among
  governmental agencies, NGOs, academic
  institutions and industry

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• At intersection of science, policy and
  applications
• 47 member countries
• Access - move data not people
• Diversity - access to all types of data
• Taxonomic Standards - need Electronic Catalog of
  Life
• Data Quality - data cleaning tools
• Interoperability - global identifiers for
  specimens, collections, etc.
• Working Together - campaign approach to setting
  priorities

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• GBIF can provide critical components of
  cyber-framework for LINNE
• In exchange, LINNE will provide data to GBIF

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• 20 European Natural History Museums and Botanic
  Gardens
• FPVI European-funded Integrated Infrastructure
  Initiative Grant
• Create integrated European infrastructure for
  researchers in the natural sciences

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• Started 2004 - five year project
• 20 institutions
• 11 national Taxonomic Facilities
• Part 1 - Access - enables European researchers to
  access earth and life science collections,
  facilities and taxonomic expertise

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• Part 2 - Networking Activities
• Complementarity - bring together information on
  collections and expertise
• Standards - long term preservation of collections
• Databases - coordinate development of collection
  databases
• New Collections - e.g. tissue samples
• New Methodologies - e.g. computerized tomography

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European Network for Biodiversity Information

• European contribution to GBIF
• Network for digitization and sharing of
  biodiversity data
• Enhance communication and cooperation among GBIF
  nodes, biodiversity institutes and related
  initiatives
• 69 Partners
• 26 Countries
• Including all major natural history collections
  and systematics institutes

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• CHRONOS
• Earth Science Community
• Dynamic, interactive and time-calibrated network
  of databases and visualization and analytical
  methodologies for sedimentary geology and
  paleobiology

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• NEON - National Ecological Observatory Network
• LINNE will provide critical baseline information
  for ecological research
• NEON will provide resources for acquiring data
  and voucher specimens and improving collections
  infrastructure at selected locations

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• Provides ideal communications forum and network
  to collections nationwide
• Provides presence in Washington D.C.
• Provides mechanism for tactical response if
  collections are threatened

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The Foundations are Already in Place

• The challenge is not to invent all of the
  necessary components de novo
• But rather, to identify what is already there
• Identify and implement the new cyberinfrastructure
  
• And integrate these components into an
  operational system
• To do this will require that we establish a
  common vision and research agenda
• And that we work as a community, worldwide to
  achieve it

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This will require a change in our scientific
culture

• Integrated, big-science approach
• Need to identify common goals and work together
• Other communities have done this, but there were
  some tough transitions
• For example, particle physicists had terrible
  problems with career recognition and rewards with
  the switch to a big science paradigm

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Challenges

• It will cost billions of dollars
• It will require Congressional action
• It will require state action
• It will require a unified user community
• It will take many years
• It will not be easy

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LINNE Steering Committee

• Hank Bart, Jr., Tulane University
• Reed Beaman, Yale University
• Lynn Bohs, University of Utah
• Brandi Coyner, Oklahoma State University
  (student)
• Linda Deck, Idaho State Museum
• Vicki Funk, Smithsonian Institution
• Diana Lipscomb, George Washington University
• Mike Mares, University of Oklahoma (co-chair)
• Larry Page, Florida Museum of Natural History
• Alan Prather, Michigan State University
• Jan and Dennis Stevenson, New York Botanical
  Garden
• Quentin Wheeler, Natural History Museum
• Jim Woolley, Texas AM University (co-chair)

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LINNE WILL PRESERVE OUR HERITAGE AND REVITALIZE
TAXONOMY LINNE WILL BE THE MOST IMPORTANT NEW
TOOL AVAILABLE TO BIOLOGISTS IN THE 21ST CENTURY
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Thank you