March 2, 2014
I’m looking forward to seeing you Tuesday for the review in preparation of Thursday’s exam (worth 15%). Please come prepared with questions other than “will this be on the test,” because it’s open-blog, paper, notes, etc, so it’s all fair game. I’ll be posting slides from last week asap.
Regarding exam structure, you can expect about 15 questions, most multi-part or requiring a few sentences or a figure. See the exam page for a bit more info, which I’ve updated with some useful review questions.
Please prepare by reviewing the central concepts and points from each lecture and from each assigned reading. Since it is open-book the exam will require application and synthesis and not just regurgitation of facts. I encourage you to spend some time with the materials so that you will be efficient with them during the exam.
You will need to review and interpret some of the literature that I reviewed in class, ie the papers that I reviewed in lecture but that we did not discuss in recitation. You will also have to draw figures that illustrate concepts or findings, since a picture is worth 1,000 words.
February 20, 2014
Dear all, very nice job dissecting the Travisano et al “Chance, History, and Adaptation” paper today. For this week’s blog, please write on:
1. Do you believe that microevolutionary models, such as the one described in this paper, can shed light on macro-scale processes? Why/why not?
2. What other (macro)evolutionary phenomenon would you like to test with microbes? For example, how would you modify the design of this experiment, and why?
In addition, if you are interested please find my recent Primer on specialization in the Lenski long-term evolution experiment, published this week in PLoS Biology. This is not required.
February 17, 2014
Our schedule has been made even more complex with the last cancellation, and I expect that many of you are wondering what you’re supposed to be doing. So here’s a review and update:
1) Please comment on a classmate’s blog (or more than one) this week, if you haven’t already. Comments should continue the conversation and thought process.
2) Visit the updated schedule at the Syllabus. This week, we will be covering what we’ve learned from a few major experiments using experimental evolution and how it applies to our understanding of evolution, in general. Your readings include 1) a review of the Lenski long-term experimental evolution project from Lenski himself, via his blog and 2) the Travisano et al study of chance and history in adaptation. We will dissect the latter reading in detail in lab.
3) Next week, I’ll be in Europe so my two PhD students will give lectures on evolution of the mutation rate (which pertains to all organisms) and evolution in biofilms. Relevant readings are posted. While I’m abroad I will post some self-assessment questions for you to begin reviewing for the exam the following week. On Tuesday 3/4, I’ll give a review of the first 1/2.
Questions? Comment here, email, or ask in class! See you tomorrow.
February 5, 2014
Tomorrow (thursday) in Lab we’ll be working on a computer laboratory that tackles “the species question” head-on. The lab is MLST-lab-2014. I’ll bring paper copies, but feel free to download and complete on your computer.
In lecture, we’ll talk about HGT, recombination, and the problem of homology. And for this weekend, I ask that you consider:
Where do bacterial species come from? And more to the point, how did your favorite bacterial species (or set of species) come to be? Please venture out into the primary scientific literature and provide a working link to the paper.
Thus far, you have done a terrific job on your blogs and I’m just now catching up. Keep it up!
February 4, 2014
Hi all, I’ve posted the updated lectures along with snapshots of the whiteboards in class. I hope these are helpful to pair with your notes. I’ll work to post slides in a more timely fashion, ahead of time if possible. Have a great snow day.
January 30, 2014
Following your terrific job of unpacking and explaining the two papers on Sulfolobus biogeographical variation, please continue your analysis on your blog this week. Specifically,
1) Offer your general perspective on the two papers, which could include pros and cons of the methods, interpretations, what you learned or was left wanting, the publication formats themselves, etc. (You need not share my obvious bias for open access.)
2) Explain how these articles altered your perspective of bacterial speciation, and whether this change applies to your understanding of the origin of species in general.
As always, comments on each other’s blogs are encouraged.
January 24, 2014
I’m sorry for the brief delay. For next week, we should be reading the Cho/Tiedje article that I didn’t yet cover, but we will discuss on Tuesday, as well as the assigned article for the first week. On your blog, please comment on how this article by Johnson et al. affects your impression of the “everything is everywhere, the environment selects” hypothesis. You might try define what a species-area curve (or a plot of beta-diversity) might look like for Prochlorococcus. Most importantly, what about this article appealed to you, what is confusing, and what questions did it raise for you?
January 22, 2014
Welcome to MicropopBio (Microbial Ecology and Evolution), this time for real!
Your assignment for tomorrow, 1/23/14 is to:
1) Create and customize your blog. Be sure to take advantage of the help links if you are confused. I know this will be just your first steps and will be a work in progress (as is this course).
2) Edit your “Hello world” post, in which you:
a. Introduce yourself: your major, career goals, why you’re taking this course, and what you hope most to learn.
b. Take a stab at the first reading that I’ll present in lecture, which is found here.
If you have questions, please comment here or email.
January 21, 2014
Welcome to Microbial Ecology and Evolution, GEN713/813, 2014. Our lecture is held T-Th 11:10-12:30 in DEM 253, and our lab/recitation is held on Thursdays in Rudman G40.
All aspects of the course (syllabus, readings, etc) will be found here at this site.
May 2, 2012
Judging from the oral presentations yesterday and the drafts, this will be a fabulous collection of grant proposals. Some final details for our collective benefit:
- A hard copy is required for the final version, due in class.
- The budget. This is supposed to be an interesting but not stressful exercise. Please make a good-faith estimate of your likely budget, spelling out how many years of person-labor at a particular rate, your bulk supplies, key services, and any special equipment that your fantasy home institution isn’t likely to have. Then add 50%, and provide that number. I am hoping to judge budgets much as “Price is Right” with a special prize (TBA) to the victor, but this is a very minor component of your proposal. It just shows that you’ve thought about how one actually might do the work you propose. You should also state what agency might be likely to support your work.
- References. Please use an accepted, consistent format such as the ASM example that I describe in the assignment and do not reference nonscientific, popular sources unless absolutely necessary.
- Design/Outcomes. For most of you, a visual model of your design and a figure of your expected outcomes can go a long way to explaining exactly what you plan to do and justify your predictions. Strongly consider including such figures.
Given that there are 12 presentations remaining, if we run long we should anticipate using our lab time beginning at 2pm to finish up. If everyone sticks at 5 minutes with 1 minute “handoffs” we could make it, but it will be very tight. I would prefer everyone has their chance to fully explain their proposal, as it is to your benefit. I also need to allow time for you to fill in your course evaluations.