Bio 551 Past

Spring Quarter 2018

Lab meeting consisting of :___________ . Link to add to the meeting agenda

When: Fridays, 9:00 - 10:30 AM. Where: Kincaid 502 (except April 6, BEACON space)

March 30: Peter - soliciting feedback on a draft of the phenotypic plasticity manuscript.

April 6: Byran - practice talk

April 13: Journal club Rodriguez-Beltran et al. 2018 Δ

April 20: Alison Feder (guest presentation!)

April 27: Graduate Student Symposium, lab meeting cancelled

May 4: Journal club Gifford et al. 2018 Δ

May 11: Peter

May 18: Reilly Poster Practice (Undergraduate Research Symposium)

May 25 "CANCELLED"

June 1: Katrina Research Update

Winter Quarter 2018

Lab meetings are Fridays from 8:00-9:30 in KIN A049

January 5: No lab meeting

January 12: Ryan McGee

  • Research update

January 19: Josh Borin

  • Research update

January 26: Recruitment Day

  • Drop in time : 9:30 - 10:30 in BEACON space
  • Quick research updates with potential recruits

February 2: Sonia Singhal

  • Paper discussion

February 9: Katrina van Raay

  • Research update!

February 16: Reilly

  • Research update!

February 23: Olivia

  • General Exam proposal

March 2: Hannah

  • Research Update

March 9: Brian

  • How is the new job? Advice from an academia to industry transition.

March 16:' Olivia

  • General Exam Practice Talk (Actual general exam scheduled for March 19th)

Fall Quarter 2017

Lab meetings are Fridays from 8:00-9:30 in KIN 502

September 29: Benjamin Kerr

  • Research update & paper discussion

October 6: All Kerr lab members

  • Lab website content creation party!

October 13: Olivia Kosterlitz

  • NSF GRFP feedback

October 20: Katrina van Raay & Alwyn Mouton

  • KvR: Research update
  • AM: Amsterdam travelogue

October 27: Hannah Jordt

November 3: Olivia Kosterlitz

November 10: Cancelled for Veterans' Day

November 17: Peter Conlin

  • Research update

November 24: Cancelled for Thanksgiving

December 1: Peter Conlin

December 8: Katie Dickinson

  • Research update

Summer Quarter 2017

Lab meetings are Fridays from 10:30-12:00 in KIN 502

June 16: Katrina van Raay

  • Life in a bubble: A bacterial insider's perspective

June 23: Luis Zaman & Katrina van Raay

  • Introduction to the new lab website / web content creation party

June 30: Robin Green & Kerr lab members

  • Nutrient-Limitation Triggers Social Behavior and Catalyzes the Formation of a Simple Community in Yeast
  • Lab website update

July 7: Cancelled

July 14: Cancelled for Microbial Population Biology GRC

July 21: Bryan Andrews

  • Research update

July 28: Hannah Jordt

  • Research update

August 4 Cancelled for BEACON Congress 2017

August 11: Cancelled

August 18: Mitchell Pesesky

  • Research update

August 24 (THURSDAY, 11:00-12:00pm): Ishay Ben-Zion

  • Research update

September 1: Benjamin Kerr

  • Research update & paper discussion: The dual landscape model of evolution and niche construction

September 8: Olivia Kosterlitz & Hannah Jordt

  • OK: Practice talk for DMS Day
  • HJ: Galapagos Islands travelogue

September 15: Cancelled for the Biology departmental retreat

September 22: Katrina van Raay & special guest

  • KvR: Research update & KITP Eco-Evolutionary Dynamics course report

Spring Quarter 2017

Lab meetings were Fridays from 10:30-12:00 in PAA A023D

March 31: Katie and Brian

  • Comments on the paper draft
  • Planning lab meetings for the quarter

April 7: Ryan McGee

April 14: Liv Kosterlitz

April 21: Cancelled for the Biology Graduate Student Symposium (GSS)

April 28: Sonia Singhal

  • Practice seminar talk -- no preparation necessary

May 5: Luis Zaman

  • Research update

May 12: Erin McClure

  • Mary Gates poster presentation

May 19: Cancelled for the Undergraduate Research Symposium

May 26: Sonia Singhal

  • Practice defense talk -- colicin evolution

June 2: Cancelled for Sonia's Defense! 11:30am

June 9: Peter Conlin

  • Nascent life cycles and the evolutionary stability of multicellularity

Winter Quarter 2017

Lab meetings were Fridays from 9:30-11:00 in KIN 502

January 6: Katie

January 13: Hannah

January 20: Hannah

  • Research Update

January 27: Peter

February 3: Sonia - paper for PRESS

February 10: BEACON Proposal Party

  • Brian: N-Step Evolutionary Programs and Addiction to Niche Construction
  • Hannah: Plasmid and host coevolution encourages the emergence of multi-drug resistance
  • Peter: Pleiotropic effects of compensatory evolution in drug-resistant Escherichia coli

February 17: Katrina

February 24: Peter

  • Feedback on fellowship proposal

March 3: Katrina

  • Emulsion update

March 10: Carrie and Sonia

  • Exit presentation on colicin stuff!

March 17: Peter

  • Research Update

Fall Quarter 2016

Lab meetings are Fridays from 9:30-11:00 in KIN 502

September 30: Quarterly lab update

  • Add a paper or two to the paper queue
  • Lab duties updates
  • EH&S survey

October 7: Research Update - Carrie

  • Note: We will meet in PAA A042C instead of our usual room.

October 14: Paper Queue

October 21: Research Update - Mitch

October 28: Paper Queue

November 4: Research Update - Brian

November 11: Canceled for Veterans Day

November 18: Paper Queue

December 2: Research Update - Sonia

December 9: Canceled

Queue

PaperTotal VotesNum Votes
Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities3.805
Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system3.405
A competitive trade-off limits the selective advantage of increased antibiotic production2.906
A Quick Introduction to Version Control with Git and GitHub2.704
Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli1.304
Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations1.303
Spatiotemporal microbial evolution on antibiotic landscapes1.004
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?0.953
Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes0.853
Forecasting Epidemiological and Evolutionary Dynamics of Infectious Diseases0.703
Biological invasions and host–parasite coevolution: different coevolutionary trajectories along separate parasite invasion fronts0.501
The Ecology and Evolution of Microbial Competition0.401
Laboratory Evolution of Microbial Interactions in Bacterial Biofilms0.201
Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast0.000
The fitness landscape of a tRNA gene0.000
Rapid and widespread de novo evolution of kin discrimination0.000

Summer Quarter 2016

Lab meetings are Fridays from 10:00-11:30 in KIN 502

June 24: Lab meeting organization

  • Beforehand: Add one or two papers to the paper list
  • Are there any dates besides August 12th when we should not meet?
  • 90-second updates

July 1: Paper

July 8: Research Updates

  • Katrina: Host-Phage Interactions and the Evolution of Novel Unicorn Horns (or TBA)

July 15: Paper

July 22: Research Updates

  • Hannah: Plasmid addiction and all that Jazz
  • Sonia

July 29: Paper

August 5: Research Updates

  • Peter: deep mutational scanning and such

August 12: Canceled for BEACON Congress

August 26: Paper

September 2: Paper

September 9: Research Update

  • #Hannah- She will give a practice talk that will feature the very latest data and story line of her project looking at how conjugative plasmids can persist in bacterial populations, despite their associated costs.

September 16: Paper

Spring Quarter 2016

Unless otherwise noted, lab meetings are on Fridays from 10:00-11:30 in PAA049.

If you are presenting, send information to the lab mailing list before Wednesday at noon.

April 1: Lab meeting organization

  • Should we meet on May 20th, which is when the undergraduate research symposium is?
  • Schedule research updates. For each research update week, we’ll have two presenters.
  • Fill the research queue with new papers. Add one or two here.
  • Each person will give a short update on their outgoing lab duty.
    • Include: what you accomplished, what needs to be accomplished, and any other notes for the new person on that duty.
    • Put links to related wiki pages or notes next to your former task on the lab duties page before lab meeting.
    • If you won’t be in lab meeting, please send me a brief summary for the first part and make sure the wiki’s been updated.

April 8: Canceled: Evolution: Making Sense of Biology (MCB Symposium)

April 15: Canceled: EVO-WIBO 2016!

April 22: Research Update

  • Hannah. TBA.

April 29: Paper:

May 6: Research Updates:

  • Sylvie. TBA.
  • Brian: THUMB Project Introduction and Status.

May 13: Guest:

May 20: Canceled: Undergraduate Research Symposium

May 27: Paper:

June 3: Research Updates:

  • Robin. TBA.
  • Luis. Big Science Extravaganza: Evolving Tiny Stuff and Counting Things with Fancy Machines.

Winter Quarter 2016

Lab meeting consisting of research update, literature queue or queue-jumping.
When: Fridays, 10.00-11.30am. Where: Kincaid 502 (except Jan 8, PAA A049D)

Paper queue and lab meeting schedule: https://docs.google.com/spreadsheets/d/1vl4eHTq_lvFDvhNugp9W99ZkFGeaIR8asrsbal-VSyw/edit?usp=sharing

Jan 8: Hannah & Sylvie : Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
Jan 15: research update ( Josh )
Jan 22: Luis & Katrina: Evolutionary Rationale for Phages as Complements of Antibiotics
Jan 29: Sylvie & Ben: Engineering microbiomes to improve plant and animal health
Feb 5: Sarah: The ecology of the microbiome: Networks, competition, and stability
Feb 12: research update ( Sarah & Katie )
Feb 19: Ben: Breaking evolutionary constraint with a tradeoff ratchet
Feb 26: Queue Jump ( Jake )
Mar 4: (GSS is all day)
Mar 11: research update ( Peter )
Mar 18: Robin: Single gene locus changes perturb complex microbial communities as much as apex predator loss

Fall Quarter 2015

Lab meeting consisting of research update, literature queue or queue-jumping.
Time: 11.00-12.20pm. Place: Kincaid A023D

Oct 2: Brian & Jake : Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations
Oct 9: research update (Hannah)
Oct 16: Katie & Robin : Evolutionary limits to cooperation in microbial communities
Oct 23: research update (Joya)
Oct 30: Sonia & _ : Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
Nov 6: research update (Sarah re: Oxford work)
Nov 13: Katrina & Katie : Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages
Nov 20: queue jump: Katrina & Ben: Background reading Additional reading to be posted Wed evening (Nov 18).
Nov 27: Thanksgiving! (canceled)
Dec 4: research update (Peter)
Dec 11: lab goals (Katrina)

Summer 2015- Lab meeting

Research updates only. Place: Kin 502. Time: 9.00-10.30

  • July 31: ( Katrina & Gordon updates )
  • Aug 21: ( Brian & Luis )
  • Sep 11: ( Jake & Sylvie )

Summer 2015

Weekly goal (please update as you go along) can be updated on the spreadsheet here: https://docs.google.com/a/uw.edu/spreadsheets/d/1MHcCunzaAFxFIFswIkcuMm_EBOuog1PtYdLw3mdAgEY/edit?usp=sharing

Group name: HACK (Currently: Hannah, Amanda, Carrie, Katrina, Katie)

Mission: This group is for beginner programmers. We will work on learning R or Python. Totally ok if you've never opened up Python or R, as Carrie said it's "no scientist left behind".

HACK Wiki

Meeting day and time: Thursdays, 11:00 in KIN 502.

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Group name: Tea with SQuEE (Brian and Katie, sometimes Luis)

Mission: Eco & Evo of QS journal club

Meeting day and time: Friday's usually around 4pm at a pub

Papers: SQuEE Zotero Group

Additional Discussion: #squee channel on Slack, also updated on Kerr Lab Meeting calendar (at least for summer)

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Group name: Methods to our Madness

Mission: Introduce each other to a new tool (technique, device, software, etc.) at each meeting

Meeting day and time: First meeting Tuesday June 16 at 11:00. Meetings added to Kerr Lab Meeting calendar.

Discussion: #methods channel on Slack

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Group name: Breakfast Club

Mission: To stay abreast of evidence-based pedagogy, focusing on higher ed STEM teaching.

Meeting day and time: Wed 8am, KIN 502

Contact Jake or Hannah for more information

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Group name: Phage Club

Mission: Read and discuss papers related to bacteriophage evolution and ecology. Impromptu brainstorming sessions encouraged.

Meeting day and time: Thurs. 11am, but please note we sometimes reschedule (and sometimes meet off campus). The Phage Club reading list and schedule will be updated regularly, but please e-mail Katrina, Sonia, or Luis to confirm time and location of meeting, just in case we forget to update something.

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Group name: pOP (aka plasmid group with Hannah and Sylvie)

Mission: Read and discuss papers related to plasmid eco/evo and horizontal gene transfer.

Meeting day and time: Fridays at 11am.

Reading list:

July 17- Frost & Koraimann (2010) Regulation of bacterial conjugation: balancing opportunity with adversity

July 2- Lau et al (2013) New quantitative methods for measuring plasmid loss rates reveal unexpected stability

June 26- Turner et al (2014) Antibiotic resistance correlates with transmission in plasmid evolution

June 19- San Millan et al (2014) Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

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Spring Quarter 2015

Revamped lab meeting.
Queues, queue-jumping, & research updates.
9-10:30 in KIN 502, unless otherwise noted.


Spring

Queue:

  1. Brian & Jake : Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations
  2. Katie & Robin : Evolutionary limits to cooperation in microbial communities
  3. Sonia & _ : Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
  4. Katrina & Katie : The costs of evolving resistance in heterogeneous parasite environments
  5. Hannah & Sylvie : Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
  6. Sylvie & _ :
  7. Peter & _ :
  8. Carrie & _ :
  9. Ben & Peter : The genetical theory of multilevel selection
  10. Amanda & _ :
  11. Robin & _ :
  12. Jake & _ :

Paper Suggestions:

  • Peter & Ben's Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory
  • Ben's Life cycles, fitness decoupling and the evolution of multicellularity
  • Character displacement and the evolution of niche complementarity in a model biofilm community - The paper focuses on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity.
  • Evolutionary limits to cooperation in microbial communities - K.Foz and group use a model to look at microbial cooperation between different strains and species.
  • Alternating Antibiotic Treatments Constrain Evolutionary Paths to Multidrug Resistance - Using experimental evolution and whole-genome sequencing, we find that alternating drugs slows the rate of increase in resistance compared with single-drug treatments, by constraining resistance mutations with trade-offs in resistance to a second drug.
  • The Time Scale of Evolutionary Innovation - But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions?
  • Importance of Positioning for Microbial Evolution - Microbes commonly form dense communities that are central to many diseases and bioremediation. Here we demonstrate a simple and general principle of living in dense communities: microbes will commonly compete to reach nutrients at the community edge, akin to plants competing for light. Our work suggests that positioning is a major basis for evolutionary competition in dense microbial communities.
  • Biogeographic Patterns in Ocean Microbes Emerge in a Neutral Agent-Based Model - A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes...The emergent patterns are substantial and suggest that microbes evolve faster than ocean currents can disperse them.
  • Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution - Mutations can fix during evolution for two reasons: they can be beneficial and fix for adaptive reasons, or they can be neutral or deleterious and fix solely by chance. Most studies focus on adaptation, where the evolving population is increasing in fitness due to a new selection pressure. Such studies have found an important evolutionary role for epistasis, the phenomenon where the effect of one mutation depends on another mutation. But adaptation only accounts for a fraction of overall evolutionary change. Here we investigate whether epistasis is as common during non-adaptive as adaptive evolution by comparing the same protein from human (under constant adaptive pressure) and swine influenza (under less adaptive pressure).
  • More bang for your buck: Quorum-sensing capabilities improve the efficacy of suicidal altruism - We use digital evolution (a form of experimental evolution that uses self-replicating computer programs as organisms) to investigate the effects of enabling altruistic organisms to communicate via quorum sensing. We found that quorum-sensing altruists killed a greater number of competitors per explosion, winning competitions against non-communicative altruists.
  • Global epistasis makes adaptation predictable despite sequence-level stochasticity - Epistatic interactions between mutations can make evolutionary trajectories contingent on the chance occurrence of initial mutations. We used experimental evolution in Saccharomyces cerevisiae to quantify this contingency, finding differences in adaptability among 64 closely related genotypes. Despite these differences, sequencing of 104 evolved clones showed that initial genotype did not constrain future mutational trajectories. Instead, reconstructed combinations of mutations revealed a pattern of diminishing-returns epistasis: Beneficial mutations have consistently smaller effects in fitter backgrounds. Taken together, these results show that beneficial mutations affecting a variety of biological processes are globally coupled; they interact strongly, but only through their combined effect on fitness. As a consequence, fitness evolution follows a predictable trajectory even though sequence-level adaptation is stochastic.
  • Pervasive domestication of defective prophages by bacteria - Several molecular systems with important adaptive roles have originated from the domestication of integrated phages (prophages). However, the evolutionary mechanisms and extent of prophage domestication remain poorly understood. In this work, we detected several hundred prophages originating from common integration events and described their dynamics of degradation within their hosts. Surprisingly, we observed strong conservation of the sequence of most vertically inherited prophages, including selection for genes encoding phage-specific functions. These results suggest pervasive domestication of parasites by the bacterial hosts. Because prophages account for a large fraction of bacterial genomes, phage domestication may drive bacterial adaptation.
  • Engineering microbial consortia: a new frontier in synthetic biology - Microbial consortia are ubiquitous in nature and are implicated in processes of great importance to humans, from environmental remediation and wastewater treatment to assistance in food digestion. Synthetic biologists are honing their ability to program the behavior of individual microbial populations, forcing the microbes to focus on specific applications, such as the production of drugs and fuels. Given that microbial consortia can perform even more complicated tasks and endure more changeable environments than monocultures can, they represent an important new frontier for synthetic biology. Here, we review recent efforts to engineer synthetic microbial consortia, and we suggest future applications.
  • Epistasis between adaptive mutations in hemoglobin - Two populations of deer mice – high and low elevation – differ in hemoglobin by 12aa in three clusters. Mix ‘n match of these three clusters show epistasis in O2-binding ability.
  • Social punishment of dishonest signallers - Paper wasp facial patterning is a signal of aggression. Signal can be manipulated with paint, trait with hormones. Four groups with ~20 pairs each: control, added paint (signal more aggression), added hormone (actually more aggressive), added both. Fig 2 shows that "added paint" group received more aggressive acts than any other. This implies social punishment when signal is higher than trait.
  • Adaptive valley crossing & recombination - Models genome structure as 4 loci: “abcd”. Uses two recombination rates, one within a “gene” (between a & b, between c & d) and another between “genes” (between b & c). With sufficiently many valley-crossings needed (e.g., 50 genes with xy local peak and XY global peak), asex gets trapped on an occasional local peak, but sex allows all global peaks thanks to recombination (Fig1).
  • Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild. - The authors experimentally measure a fitness landscape in populations of wild pupfishes. They relate their findings to the populations' adaptive radiations and their tendency towards ecological generalism.
  • Explaining microbial genomic diversity in light of evolutionary ecology. - Review paper that suggests that much of microbial genetic diversity is due to social and ecological interactions. Population structure, niches, social cheating, quorum sensing are all talked about in this nicely written and easy to follow paper.
  • The winnowing: establishing the squid–vibrio symbiosis. - Really fun review paper that covers everything you wanted to know about the squid-vibrio symbiosis.
  • Genetic information transfer promotes cooperation in bacteria. -Talks about how horizontal gene transfer can favor cooperation. Authors compare structured and well-mixed environments to better understand the prevalence of cooperative genes on mobile elements.
  • A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait.- Authors look at how epistatic interactions evolve in real time in specific biological systems. They characterize how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus.
  • Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Population- Authors demonstrate a coupling between population dynamics and the evolutionary dynamics of a “social” microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene.
  • The evolution of plasmid-carried antibiotic resistance
  • Niche engineering demonstrates a latent capacity for fungal-algal mutualism

Winter Quarter 2014

This quarter is the first of a revamped lab meeting, in which we have a paper queue (with pilot & copilot), queue-jumping for emergent lab fun, and once-a-month research updates. We are meeting 9-10:30, in KIN 502.

Fall Quarter 2014

This quarter we are doing a pairwise journal club of current papers, with once a month research updates. We are meeting 11-12, in the BEACON space.

Summary: Two populations of deer mice – high and low elevation – differ in hemoglobin by 12aa in three clusters. Mix ‘n match of these three clusters show epistasis in O2-binding ability.

Summer Quarter 2014

This quarter we are working through Sex & Death (Sterelny & Griffiths 1999), which is an intro to the philosophy of biology. We are meeting 10-11, in KIN 502.

  • JUN 20: Chapters 1, 2: Intro & The Received View - Ben
  • JUN 27: Chapter 3: Gene's Eye View - Jake
  • JUL 4: enjoy your BBQ
  • JUL 11: Chapters 4, 5: Organism Strikes Back & Developmental Alternative - Sylvie
  • JUL 18: Chapters 6, 7: Mendel and Molecules & Reductionism - Hannah
  • JUL 25: Chapter 8: Organisms, Groups, and Superorganisms - Sarah
  • AUG 1: Chapter 9: Species - Katrina
  • AUG 8: research updates
  • AUG 15: no lab meeting this week
  • AUG 22: Chapter 10: Adaptation, Perfection, Function - Sonia
  • AUG 29: Chapter 11: Adaptation, Ecology, and the Environment - Brian & Katie
  • SEPT 5: Chapter 12: Life on Earth: The Big Picture - Luis

Spring Quarter 2014

This quarter we are doing a pairwise journal club of classic papers, with once a month research updates. We are meeting 10-11, in KIN 502.

Bonus papers
(papers submitted but not chosen this quarter)

  • A Strategy of Win-Stay, Lose-Shift That Outperforms Tit-for-Tat in the Prisoner’s Dilemma (Nowak 1993)
  • The Small World Problem (Milgram 1967)
  • Developmental Plasticity of Species Differences (West-Eberhard 2005)
  • The Prophage and I (Lwoff 1966)
  • Evolutionary Rate at the Molecular Level (Kimura 1968)
  • Evolutionary Games & Spatial Chaos (Nowak & May 1992)
  • Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms (Woese & Fox 1977)
  • The Origin & Behavior of Mutable Loci in Maize (McClintock 19xx)
  • Is Wright’s Shifting Balance Process Important in Evolution? (Coyne 1999)
  • Harold & the Purple Crayon (Johnson 1955)

Winter Quarter 2014

This quarter we are doing a pairwise journal club (2 "hosts" per week!), with once a month research updates. We are meeting 10:30-11:30, in basement room A023D.

Bonus papers
(papers submitted but not chosen this quarter)

Fall Quarter 2013

This quarter we are having a journal club, with special guest Ben Skyping in from sabbatical once a month for research updates. We are meeting 11:30-12:30, in HCK 312.

Summer Quarter 2013

This quarter we are going to be reviewing basic computational skills (using the shell, using the wiki, basic programing using python and R, data analysis, figure generation, using cloud computing, object-oriented concepts, etc.).

  • 21 JUN: Orientation (wiki introduction, basic shell, downloading software)
  • 28 JUN: Reading, writing, using and manipulating CSV files using Python, R, and Excel
  • 05 JUL: Python basics (basic data types [integers, floats, strings], lists, conditionals, loops)
    • Connect to this link, and under the section called "Learn the Basics" check out the tutorials from "Hello,World!" to "Loops" and try your hand at the exercises
    • If you have the time, you can also check out this introductory Python tutorial video by Jessica McKellar
  • 12 JUL: More Python basics (functions, dictionaries, sets)
    • Make sure you understand the tutorials from last week.
    • You might find it helpful to go through our notes from last week. Try to solve the problems listed there: we will spend the first few minutes of next week sharing solutions.
    • Connect to this link, and read the tutorials for "Functions" and "Dictionaries" (under the section "Learn the Basics"), as well as "Sets" (under the section "Advanced Tutorials") and try your hand at the exercises.
    • Download the code for our meeting here and the colony counts to analyze here.
  • 16 JUL: Object-oriented programming in Python (classes, objects, and inheritance)
  • 02 AUG: Program design in Python (writing clear and reusable code; constructing libraries)
  • 09 AUG: Special libraries in Python (NumPy, MatPlotLib, NetworkX, etc.)
  • 23 AUG: Using the cloud (running Python)
  • 30 AUG: Introduction to R (basic data types, conditionals, loops, functions, libraries)
  • 06 SEP: Analyzing data and making figures (R/Python)
    • Tradeoff data from class (csv)
  • 20 SEP: Special topics (testing code, regular expressions, etc.)

Spring Quarter, 2013

This quarter we are reading the primary literature. We are discussing the following papers:

  • April 5 Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space
  • April 12 Does experimental evolution reflect patterns in natural populations?
  • April 19 Improved use of a public good selects for the evolution of undifferentiated multicellularity & Experimental evolution of multicellularity using microbial pseudo-organisms
  • April 26 Evolution of Stress Response in the Face of Unreliable Environmental Signals
  • May 3 Public good dynamics drive evolution of iron acquisition strategies
  • May 10 Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies
  • May 17 Canceled
  • May 24 Topological Signatures of Species Interactions in Metabolic Networks
  • May 31 Evolutionary change during experimental ocean acidification
  • June 6 Cause and Effect in Biology Revisited: Is Mayr's Proximate-Ultimate Dichotomy Still Useful?

Spring 2013 Lab Meeting Papers

Winter Quarter, 2013

This quarter we are giving progress reports on the various on-going projects in the lab as well as discussing one paper in each lab meeting.

Sign-up to present at lab meeting

Note: Remember that this is a public page. Do not attach published works, only links. Password-protected uploads are can be put here.

Fall Quarter, 2012

This quarter we are giving progress reports on the various on-going projects in the lab.

Sept 28: Lab Orientation (meet in the lab), SQuEE, and Brian Connelly

Sign-up to present at a lab meeting

Sign-up for one-on-one meetings

Spring Quarter, 2012

This quarter we are reading Robustness and Evolvability in Living Systems by Andreas Wagner.

Click here for scanned pdfs of every chapter in the book

March 30th: Chapters 1 & 2 (Josh)

April 6th: Chapters 3 & 4 (Jake)

April 13: Chapters 5 & 6 (Carrie)

April 20: Chapters 7 & 8 (OPEN)

April 27: Chapters 9 & 10 (Ben)

May 4th: Chapters 11 & 12 (OPEN)

May 11th: Chapters 13 & 14 (Peter)

May 25th: Chapters 15 & 16 (Sonia)

June 1st: Chapters 17 & 18 (Frazer)

June 8th: Chapters 19 & 20 & Epilogue (Katie)

Winter Quarter, 2012

This quarter we are reading Only A Theory: Evolution and the Battle for America's Soul. Please sign up for a week and link to an supplemental material paper.

Jan 13th: Chapter 1 and Wiki Tutorial (Josh Nahum)

Jan 20th: Cancelled due to weather

Jan 27th: Chapter 2 & 3 and The Evolutionary Origin of Complex Features (Ben Kerr)

Feb 3rd: Chapter 4 and A Draft Sequence of the Neandertal Genome (Neem)

Feb 10th: Chapter 5 and Oxygen and the Evolution of Complex Life (Sonia)

Feb 17th: Chapter 6 (Carrie)

Feb 24th: Cancelled

Mar 2nd: Chapter 7 (Peter)

Mar 9th: Chapter 8 and Using Avida-ED for Teaching and Learning About Evolution in Undergraduate Introductory Biology Courses (Josh Nahum)

Ben's Meeting Schedules

Beacon Schedule

BEACON Meeting Schedule