Reading and Discussing


    Week Two (August 26)

    Meet and greet.

    Discuss HIV as an example of how evolution fundamentally works. This is our primary learning goal: drift, selection, movement, recombination. Of course, we also have to deal with the evolution of pathogenicity itself! First, lets read about identifying how much a pathogen is evolving over time:

    Download file "Biek_ea_15.pdf"

    Everybody will read this paper - it isn't so long. And this week, everybody will also read this paper on the "Science of Scientific Writing", because it will help us all see better ways to organize our OWN writing as well as understand when a paper is hard to understand because they haven't communicated well with us!

    Week Three (September 2, September 9)

    Discuss the Biek et al paper, but is evolution always associated with an outbreak?

    For next week, read the paper by Olabode et al:
    Download file "Olabode_ea_15.pdf"

    and also each of you will pick a theme that you are going to follow for the rest of the semester. Are you interested in human disease? Zoonoses (diseases that move from animals to humans)? The pathogens themselves? Microbes? Viruses? Parasites? Resistance? Drugs and therapy?

    Week Four (September 23)

    Another good paper: how mutation and spatial dynamics interact so we can learn about outbreaks:
    Download file "PNAS-2005-Real-12107-11.pdf"
    Remember, each week your graded contribution involves adding to the wiki - including improving explanations your classmates have put on the wiki, adding information you have found useful or interesting related to "evolution" and "disease" and how they interact!

    September 30

    Following on last week's paper - where we explored genealogical data over space - here is a very recent approach to understanding genetic variation in flu virus with a web tool to visualize the dynamics over time!
    Download file "neher-nextflu.pdf"

    October 7

    Another from the same lab group, using similar approach, as last week - to help us get this sorted in our heads!
    Download file "bedford-global-circulation.pdf"

    October 14

    And finally (from this lab group), a paper that hopefully we can use to grasp how selection affects variation in virus populations.
    Download file "bedford-tree-topology.pdf"
    Note that next week (October 21) there will be no class, as my PhD student is defending!

    October 28

    How do you identify a pathogen in an emerging disease, in a poorly-known system?
    Download file "PNAS-2014-Hewson-17278-83.pdf"

    November 4

    More from the marine world...Disease is a symptom, which is a phenotype! First read this, then read:
    Download file "PNAS-2015-Pettay-7513-8.pdf"

    November 11

    What about the dynamics that the pathogen itself faces in maximizing survival... or fecundity.... not both?
    Download file "Wasik_et_al-2015-Evolution.pdf"

    November 18 our classroom is needed for another PhD defense; no classes after this date!!!!

    How biodiversity - an evolutionary outcome - interacts with emergence and transmission of disease
    Download file "nature09575.pdf"


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