I encourage the class to read through the papers assigned to Groups 3 and 4 before Tuesday so that they are prepared to appreciate the presentations, and enjoy what are interesting papers. The papers are listed on the Student Presentations webpage and can be downloaded from the Sakai 174 webpage, under Resources.
A brief overview and motivation for these three papers:
I will try to assign papers for the last two groups during the next few days, but also encourage those groups to select a paper of their own. One paper I was thinking to assign would be about the status of "artificial digital life", attempts to create an entire ecology of "organisms" that breed, mutate, and compete for limited resources (in a computer's read-only-memory or RAM), and what kinds of insights about real life one can get from such simulations. (This paper could be hard to read if you don't know how computers work.) Another paper I was thinking about would be about the theme of how extremely simple mathematical models can generate complicated dynamics (this is the field of nonlinear dynamics and automata theory), and so complicated behavior in biological systems does not necessarily imply that an underlying model has to be complex. (And what does "complex" mean anyhow?)
Note: I will be out of town from November 23 until the evening of Monday, November 28, so will unfortunately not be able to meet with the three groups to discuss slides until Tuesday morning, November 29. So I would encourage the three groups that present on the 29th to look over the assigned papers and make a pass at putting slides together by November 22 of next week, in which case I can meet with you before I leave town.
As an aside, Kauffman is a scientific visionary and highly creative scientist and has made several major contributions in biology and biophysics, most of you should find his entire book stimulating to read.
Also look up and briefly describe a biophysics-related "quantitative biology" or q-bio preprint from arXiv. ArXiv was a grand successful experiment, about ten years old now, in Internet communication invented by the physics community to make the sharing of physics-related preprints easy. The arXiv papers are indeed preprints, which means that they have not been refereed so may contain errors or be unclear. (Refereeing almost always greatly improves a paper.) The advantages are that other scientists can find out about some research result within weeks after the discoverty (some journals can take over a year for a submitted paper to be approved and published), and scientists can find out about a result without having to subscribe to journals, many of which are quite expensive (thousands of dollars per year for the top journals). Further, researchers with limited funds, e.g., in some third-world countries, can get their ideas out without paying what can be expensive journal page charges (several hundred dollar per page). In certain areas of science, arXiv has become a major way to share advances and a few fields like string theory rely so heavily on arXiv that sometimes the preprint never gets published beyond arXiv. There are ongoing discussions on whether journals should be eliminated and most scientific papers submitted via an arXiv-like server.
I also would like to encourage you to attend biophysics seminars and write about what you learned in your blogs. You can replace writing about a journal article with a discussion about a seminar that you attended.
Note: all future presentations must last 20 minutes, no less and no more. Two of the recent presentations lasted substantially less than 20 minutes, which was a missed opportunity to present information or to explain things further to the class. Practice your presentations: if your talk lasts less than 20 minutes, add some slides or spend more time explaining the details on your slides. It is better to have extra slides that you can skip than not have enough slides. If your presentation runs short, your grade will be penalized.
Unlike the case for the other journals you have looked at so far, articles in Nature are not explicitly labeled as "biophysics" so it will take more effort to find such articles. One way is to look through the "News & Views" section of recent Nature magazines; this section identifies and explains at a nontechnical level particularly interesting papers. More generally, the "News & Views" is a good way for you to keep up with progress in several scientific fields, which is important for people interested in an interdisciplinary field like biophysics.
Because Groups 3-5 have more time to prepare than did Groups 1 and 2, I will be grading more strictly this time around.
As a reminder, your blog entry for this week (due by Sunday night) should discuss the presentations by Groups 1 and 2 and describe briefly some paper that you find interesting in the Biophysics Journal.
Note: It is easy to walk right by the door in the West Union Building that leads to the Faculty Commons second floor. The door is at the corner of the West Union Building that is closest to the East-West bus stop (the corner furthest to the right on the Duke map).
When setting up groups, I mixed class members by year and by backgrounds (strengths in biology, chemistry, math, and physics), so that members of each group can help each other as they prepare their presentations.
The first two groups will lead off the group presentations on Tuesday, September 20.
Group 1 will discuss the following paper:
The primary paper was one the papers that created the field of "synthetic biology", in which scientists modify biological genetic circuits to achieve various desired capabilities.
Group 2 will discuss two related papers
The primary paper is an impressive application of the biophysics technology of microfluidics that greatly increased the clinical ability to detect cancer cells in a patient's blood. The second paper is a non-technical overview about microfluidics.
Each presentation will last 20 minutes with about 5-10 minutes for discussion.
The day of presentation, I will use a random number generator to choose which member of a group gives the actual presentation. So each member of the group will need to be ready to give the presentation, and the members of each group should help each other to give a polished, insightful, and interesting summary of the papers. All members of a group will receive the same grade for the presentation. The first two group presentations will get somewhat higher grades in reward for going first.
I will be assigning topics and papers to the other groups later this week.
Each group that will be giving a presentation should meet with me for about 30 minutes outside of class, once early in the week to get oriented for their presentation, and a second time before the Tuesday of the presentation, to get some feedback on their slides.
I would like all students in 174S to print these two papers out,
and spend about an hour (no more) looking them over before next
Tuesday's class. (I put copies of these papers on the
class Sakai site so you
can easily access them.) These papers will likely have parts that are
over your head (I for one don't understand all the details) but that
is not a problem, most scientific papers are hard for people, even
professors, to understood fully the first time. So when reading these
two papers you should
As you read through these papers, do so actively, with a pen in hand so you can make annotations on the papers about unfamiliar vocabulary, interesting points, questions you might want to ask Prof. Truskey, etc.
For this seminar and later in your scientific career, it is important you learn how to get the gist of a scientific paper efficiently, there simply is not enough time to read all the scientific papers that are published each week, even those related to one's own areas of interest.
The above recommendations about how to read a journal article will also be important when your group leads a discussion about a journal article. Often, an audience is most interested in the implications and significance of some result rather than all the technical details that led to the result, and this will guide how you want to summarize a paper for the class.
Some of my slides we did not get around to discussing in class. One of my slides was about the movie Inner Life of a Cell which I had planned on showing in class and which you should view on your own if you have not seen it previously. It is a supercomputer simulation that illustrates many biophysical events related to the functioning of a white blood cell (leukocyte). If you search the Internet, you can find a longer version of this video with narration, which describes what you are looking at. As a challenge, can you identify one or more serious flaws of this movie?
Note: you will want to take some notes during each class. Your notes can lead to a question for the 1-minute questionnaires, will help you write your required weekly blog entry about the most recent 174 class you attended, give you a chance to write down vocabulary or ideas with which you are not familiar, and help you remember interesting points made by your classmates or by myself.