Lectures

Most classes will include the following components: (1) Lectures by Prof. Newman and Prof. McFall-Ngai to cover the micro- and macro-biological worlds, respectfully. You are welcome to record the lectures, but recordings will not be made available on the website. Course notes, however, will be posted here after each class. (2) At some point during the class, an iClicker quiz will be given. Each quiz will have two multiple-choice questions: one question will cover material that is presented that day; the other will concern material from any previous lecture or reading assignment to encourage you to continuously review what you are learning. These questions may be asked at the same time or separately. You will receive full credit for the quiz if you get either answer correct, half credit for completing it whether your answers are right or not, and zero credit if you do not take the quiz. The correct responses will be given to you afterwards. We encourage you to ask a question during class at any time if you are confused about the material being presented.

Most classes will include the following components:


(1) Lectures by Prof. Newman and Prof. McFall-Ngai to cover the micro- and macro-biological worlds, respectfully. You are welcome to record the lectures, but recordings will not be made available on the website. Course notes, however, will be posted here after each class.

(2) At some point during the class, an iClicker quiz will be given. Each quiz will have two multiple-choice questions: one question will cover material that is presented that day; the other will concern material from any previous lecture or reading assignment to encourage you to continuously review what you are learning. These questions may be asked at the same time or separately. You will receive full credit for the quiz if you get either answer correct, half credit for completing it whether your answers are right or not, and zero credit if you do not take the quiz. The correct responses will be given to you afterwards. We encourage you to ask a question during class at any time if you are confused about the material being presented.

Lectures will be held Tuesdays and Thursdays, 1:00 – 2:30 pm in Kerckhoff 119


Week 1 - Life from 30,000 feet – basics about biotic systems

Lecture 1 (Apr 3) - Orientation to the course/life’s organization/evolution as the unifying principle

  1. -Possible inspiration for writing assignment as referred to in Margaret’s lecture: http://www.youtube.com/watch?v=_UZ5u5sN1WQ

  2. -Lecture 04/03/12: Lecture_1.pdf

- Margaret’s typed Lecture 1:  MMN 4-3 TYPE.pdf


Lecture 2 (Apr 5) - The structure of life forms: The cell as the unit of life/the eukaryotic cell/the patterns and consequences of multicellularity

- DNA folding (Paul Rothemund TED talk): http://www.ted.com/talks/paul_rothemund_details_dna_folding.html

- Lecture 04/03/12: Lecture_2.pdf

- Typed Lecture 2: Lecture-Apr 5 TYPE.pdf


Reading assignments:

  1. -Editorial (2011) “Microbiology by numbers.” Nature Reviews Microbiology 9: 628.

  2. -Cohen, Joel E. (2004) “Mathematics is Biology’s New Microscope, Only Better; Biology is Mathematics’ Next Physics, Only Better.” PLoS Biology  2, e439: 2017-2023.

  3. -Finkel, Steven E. & Kolter, Roberto (1999) “Evolution of microbial diversity during prolonged starvation.” PNAS USA 96:4023-4027.


Week 2 - History of the biosphere and forces shaping its trajectory

Lecture 1 (Apr 10) - Origins

  1. -6th mass extinction movie: http://www.calloflife.org/p-trailer.htm

- Find some of the movies referred to in Dianne’s lecture here: http://exploringorigins.org

  1. -Lecture 04/10/12: Lecture_3.pdf

  2. -Dianne’e typed Lecture 3: DKN 4-10 TYPE.pdf


Lecture 2 (Apr 12) - Mechanisms underlying continuing evolution of the biosphere/patterns of radiation

  1. -Video about Biophysicist John Dabiri : http://www.youtube.com/watch?v=x2audOlniaQ

  2. - Extra Credit Opportunity 4/12/12: Extra Credit due 4-17-12.pdf

  3. -Lecture 04/12/12: Lecture_4.pdf

  4. -Typed Lecture 4:  Lecture-Apr 12 TYPE.pdf


Reading assignment:

- Pace, Norman R., et al. (2012) “Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life.” PNAS USA 109: 1011-1018.


Week 3 - Sensing the environment, integrating the information, and responding

Lecture 1 (Apr 17) - Sensing, integrating and responding to the environment

- Interesting movie on Myxobacteria: Wave Patterns in Myxobacteria.mov

  1. -Bonnie Bassler TED talk on Bacterial communication:

http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html

  1. -Lecture 04/17/12: Lecture_5.pdf

  2. -Typed Lecture 5: Lecture-Apr 17 TYPE.pdf


Lecture 2 (Apr 19) - Consequences – Effects on population/community dynamics and behavior

Guest lecturer: Prof. Kenneth Nealson, USC

  1. -Lecture 04/19/12:

    - Quorum Sensing: Nealson_Part_1.pdf

    - Extracellular Electron Transport: Nealson_Part_2.pdf


Reading assignment:

- Alon, U (2007) “Robustness of protein circuits: The example of bacterial chemotaxis.” In: An Introduction to Systems Biology, Chapman & Hall/CRC. 137-159.


Week 4 - Resisting perturbation and damage from the environment/energy acquisition

Lecture 1 (April 24) - Exchange with the environment: Protecting the home front

Guest lecturer: Prof. Ann Hirsch, UCLA

- TED talk about the fastest animals: http://www.ted.com/talks/sheila_patek_clocks_the_fastest_animals.html

- Chameleon feeding movie: http://en.evilox.com/videos/cameleon-slowmotion

- Lecture 04/24/12:

        - Ann Hirsch Guest Lecture: Ann Hirsch Lecture.pdf

        - Margaret’s Typed Lecture 7: MMN_4-24 TYPE.pdf


Lecture 2 (Apr 26) - Overview of metabolism and nutrient acquisition

- Lecture 04/26/12: Lecture-Apr 26 TYPE.pdf


Reading assignment:

- Stipp, David (2012) “A new path to longevity.” Scientific American, 32-39.


Week 5 - Metabolism

Lecture 1 (May 1) - Mechanisms of energy acquisition

Guest lecturer: Dr. Nicky Caiazza, Synthetic Genomics, Inc., http://www.syntheticgenomics.com

  1. -Lecture 05/01/12:

        -DKN Lecture 9: DKN_5-1.pdf

        -Caiazza Guest Lecture: Nicky_Caiazza_5-1.pdf


In class EXAM I (May 3)


Reading assignment: none


Week 6 - Mechanisms underlying persistence of life forms: The molecular basis for growth and reproduction

Lecture 1 (May 8) - Mechanisms underlying the central dogma

- Linus Pauling and the Race for DNA: http://osulibrary.orst.edu/specialcollections/coll/pauling/dna/index.html

- Interview with Nobel Laureate, Venki Ramakrishnan: http://www.youtube.com/watch?v=vp0LYz5D8Yc

- Musical Ribosome Movie: Musical Ribosome 5-8-12.mov

- Dianne’s typed Lecture 10: DKN_5-8 TYPE.pdf

- Margaret’s typed Lecture 10: MMN_5-8 TYPE.pdf


Lecture 2 (May 10) - Mechanisms of gene exchange/cell division/cell cycle

  1. -Epigenetics application to cancer research movie: http://www.hulu.com/watch/231472/stand-up-to-cancer-meet-su2cs-scientists-epigenetics-dream-team

  2. -Central Dogma Song: http://www.youtube.com/watch?v=_Q2Ba2cFAew

  3. -Extra Credit Opportunity 5/10/12: Extra Credit due 5-15-12.pdf

  4. -Lecture 05/10/12: Lecture_11.pdf

  5. -Typed Lecture 11: Lecture-May 10 TYPE.pdf


Reading assignment:

- Collins, James (2012) “Synthetic Biology: bits and pieces come to life.” Nature 483: S8-10.


Week 7 - Patterns of development

Lecture 1 (May 15) - Cell determination and differentiation

- Rich Losick (Harvard), Part 1:  http://www.youtube.com/watch?v=rj5cqkMtCjg

- Lucy Shapiro (Stanford), Part 1: http://www.youtube.com/watch?v=JA5j8QzAz0w

- Lucy Shapiro (Stanford), Part 2: http://www.youtube.com/watch?v=nI7PtwhS49o

  1. -Lecture 05/15/12: Lecture_12.pdf

  2. -Typed Lecture 12: Lecture-May 15 TYPE.pdf


Lecture 2 (May 17) - The ecological and evolutionary mechanisms underlying developmental patterns

- Rich Losick (Harvard), Part 2: http://www.youtube.com/watch?v=ERMcIvzNrVw

  1. -Extra Credit Opportunity 5/17/12: Extra Credit due 5-22-12.pdf

  2. -Typed Lecture 13: Lecture-May 17 TYPE.pdf


Reading assignment:

- Sultan, Sonia E. (2007) “Development in context: the timely emergence of eco-devo.” Trends in Ecology and Evolution 22: 575-582.


Week 8 - Living with others - populations and communities

Lecture 1 (May 22) - Patterns of diversity – predator/prey dynamics/competition for resources

  1. -Lecture 05/22/12: Lecture_14.pdf

  2. -Typed Lecture 14: Lecture-May 22 TYPE.pdf


Lecture 2 (May 24) - Syntrophy and other forms of symbiosis

  1. -NO LECTURE


Reading assignment:

- Fuhrman, Jed A. (2009) “Microbial community structure and its functional implications.” Nature 459: 193-199.


Week 9 - Ecosystems biology – global issues

Lecture 1 (May 29) - Biogeochemical cycling/sustainability/Gaia

  1. -Lecture 05/29/12: Lecture_15.pdf

  2. -Typed Lecture 15: Lecture-May 29 TYPE.pdf


Lecture 2 (May 31) - Ethics and biology/synthetic biology and other fun topics

Guest lecturer: Myles Jackson, New York University

- Movie about genetic privacy: http://www.youtube.com/watch?v=zR0KzKfTa7E

- Myles Jackson Lecture Part 1: Myles Jackson Intro.pdf

- Myles Jackson Lecture Part 2: Myles Jackson-Race and Genes.pdf


Reading assignment:

- Hardt, Marah J. & Safina, Carl (2010) Threatening ocean life from the inside out. Scientific American: 66-73.


Week 10 - Horizons in biology and the associated ethics

Lecture 1 (June 5) - Our imperiled planet – the effects of climate change/feasibility of proposed solutions (e.g., geoengineering/conservation biology)

  1. -Typed Lecture 17: Lecture-Jun 05 TYPE.pdf


In class EXAM 2 (June 7)


Reading assignment:

- Lunshof, Jeantine E, et al. (2008) “From genetic privacy to open consent.” Nature Reviews Genetics 10.1038: 2-7.


FINAL ORAL EXAM (June 8, 13 or 14)