Teaching science in Second Life

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A CDE seminar held on 19/4/11: Clare Sansom, structural biologist, Web 2.0 enthusiast and CDE Fellow, will then illustrate how the immersive virtual world, Second Life, can be used to illustrate …

A CDE seminar held on 19/4/11: Clare Sansom, structural biologist, Web 2.0 enthusiast and CDE Fellow, will then illustrate how the immersive virtual world, Second Life, can be used to illustrate molecular structures and teach molecular sciences, and discuss its application in teaching other highly "visual" disciplines.

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  • 27

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  • 1. Teaching Science in Second Life Dr. Clare Sansom Centre for Distance Education London, 19 April 2011
  • 2. What is Second Life?
    • A fully immersive “online virtual world”
    • Users explore the world and interact with each other as “avatars”
      • Launched 2003: basic service (only) free
      • More than 20 million user accounts (2011 data)
        • ~ 1.5M “active” accounts
    • HE institutions with significant presence include
    Indiana University The Open University Imperial College, Medicine
  • 3. Objects in Second Life
    • Second Life includes software for creating objects
      • A basic “rezzer” to build 3D objects from simple geometric shapes (primitives, or “prims”)
      • Software to enable avatars to interact with objects
      • More complex, sculpted prims and textures
      • Software for creating special types of object
        • (e.g. molecular structures)
  • 4. Molecules in Second Life… Model of the protein cytochrome C created in Second Life using a “Protein Rezzing Toolkit” Software © Peter Miller, Andrew Lang, Troy McConagh
  • 5. My Background: Birkbeck’s Distance Learning MSc
    • Modular MSc Structural Molecular Biology launched 2001
    • First Internet-only course launched 1995
      • Principles of Protein Structure
      • First completely web-based formal University course in biological sciences in the UK
    • Students have come from 5 continents
      • 1998-9: ~40 students from central / eastern Europe, funded through Open Society Foundation
      • 2007-9: ~25 students from southern Commonwealth countries, funded through Commonwealth Scholarships
  • 6. Immersive Worlds: The Beginnings
    • For 10 years until 2008 Birkbeck students and tutors met in a MUD
      • MUD = M ulti U ser D imension
      • ~ “rich” chat room type experience
      • An Internet environment in which participants move around and interact with each other
        • Using 1980s technology
      • Mostly text-based; Web interface popular
        • Initially used “BioMOO”
        • Replaced with dedicated server at Birkbeck
  • 7. BioMOO: A Precursor to Second Life?
    • A mainly text based “virtual world”
    • Included different environments including “tutorial rooms”
    • Some students developed
    • Some (limited) use of objects
      • e.g. transcripts of tutorial sessions
    • Public area: tutorials could be “gatecrashed”
    BioMOO “screen shot” : 1997
  • 8. Web 2.0 Social Software at Birkbeck
    • Project funded for one year (2008) by Centre for Distance Education
    • Explored use of Web 2.0 tools
      • Blog
      • Wiki
      • Social bookmarking
      • Instant Messenger
        • Instead of or in addition to the existing MUD?
      • Second Life
    • Do they enhance our students’ learning? How? Which work best?
    • Concentrating on one cohort:
      • Students taking Principles of Protein Structure 2007-8
  • 9. Birkbeck Structural Biology in Second Life
    • Tested Second Life with a “focus group” of past and present students…
      • … including one Commonwealth Scholar, and one ex-student with Asperger’s syndrome
      • Held informal discussions
    • Demonstrated “walk through” molecules illustrating aspects of 3D structure
      • Did not attempt to construct our own!
  • 10. Focus Group Conclusions
    • Almost all students had no prior experience of immersive virtual worlds
    • Students’ experiences of Second Life varied enormously
    • Many found it impossible to use
      • Almost all Commonwealth Scholars
      • Industry-sponsored students using sites protected using firewalls
    • More found it “intriguing” and quite useful in learning
    • A few were hooked
      • Including the former student with Asperger’s Syndrome
    • Second Life depends on state-of-the-art hardware, and fast Internet lines
      • Should that prevent its adoption or merely modify the way we use it?
  • 11. Interacting with Molecules and Biological Systems
    • Other groups are further advanced:
    • Peter Miller (University of Liverpool, UK)
      • Visualising Microbial and Molecular Structures
    • Jean-Claude Bradley (Drexel University, USA)
      • Visualising Organic Chemistry
    • Andrew Lang (Oral Roberts University, USA)
      • Student Projects: “Learning by Doing”
  • 12. Molecular and Microbial Structures
    • Second Life used in undergraduate microbiology “core skills” course
    • Student projects have included
      • Illustrating mechanisms through models of bacterial cell walls
      • Building displays describing the structure and properties of genes in Mycobacterium tuberculosis
      • Annotating a 160m-diameter representation of the M. tuberculosis genome
      • Visualising human gut biota
  • 13. Images of Genes and Proteins Part of the M. tuberculosis “giant genome” Lysin B from mycobacteriophage D29: A “multi-sculpted” protein © Peter Miller Genes are touch sensitive Menu of information revealed on clicking
  • 14. Visualising Organic Chemistry
    • Interactive 3D models of organic molecules can complement other types of modelling
      • Complexity of the modelling interface limits its use
      • Tools to input molecular descriptions as SMILES strings have improved ease of use
    1-methyl histidine SMILES: CN1C=C(N=C1)CC(C(=O)O)N
  • 15. Serotonin Second Life representation of serotinin created from its SMILES string using the ORAC program © Jean-Claude Bradley C 10 H 12 N 2 O
  • 16. “ The Spectral Game”
    • Students score points by identifying molecules from their NMR spectra
    © Jean-Claude Bradley
  • 17. “ Learning by Doing”
    • Students at Oral Roberts University learn by building Second Life representations of biological and chemical entities
      • Building scale models of hydrogen atom orbitals
      • Illustrating Conway’s Game of Life
      • Demonstrating algal bloom
    • Public domain tools built by collaborators regularly used by students
      • Protein structure rendering tools
      • ORAC molecular rezzer (using SMILES strings)
  • 18. Problems in Second Life?
    • Second Life’s developer, Linden Lab, is cutting down on discounts and perks for educational customers
    • Steep learning curve is still a serious problem!
    • Nature ’s four-year experiment using Second Life for lectures and discussions ended in 2010
    • Solutions…?
      • A “basic” version of Second Life for beginners
      • Education-focused virtual worlds
        • Commercial examples include ReactionGrid
      • Open source solutions
        • Open Sim
      • To be explored in another lecture in this series
  • 19. Acknowledgements
    • At Birkbeck:
      • David Moss, Peter Murray-Rust and Alan Mills, distance education pioneers
      • Dave Houldershaw, technical coordinator
    • In Second Life:
      • Peter Miller (avatar Graham Mills)
      • Andrew Lang (avatar Hiro Sheridan)
      • Jean-Claude Bradley (avatar Horace Moody)
      • (I am Rosalind Heliosense)