Monday, May 23, 2011

The dark side

I just bought a MacBook Pro. Believe me, this is Breaking News. I have been a PC person for more than 20 years. Or I should say a PC owner. The first computer I worked with was actually a Mac, and over the years I had to use them for a number of applications in Flow Cytometry or in labs where that was the standard. So I know how to use them, and have consistently appreciated how everything artsy seems to be better for Macs than for PCs.  And they are cool and sleek.
So why did I not buy one before?
Two simple reasons: the cost and the fear of incompatibility.
The first is rather self-explanatory. Say what you want, but Apple computers are more expensive than PCs. Until the last minute before I hit the Checkout button, every comparison, feature by feature, was cheaper for PCs. My baby here is in fact refurbished, which made it less outrageous. But still.
The other comes with my experiences in the past. I still remember when working in groups where some people were PC and others Mac, the nightmare it was to make all documents and pictures visible to all and look alike. To the day of today, some students will send their projects in certain formats that I cannot open, and they turn to be Mac formats. 
Last but not least, I dislike Apple's proprietary policies and closed systems. 
So why did I do it now?
My main reason is the need for a robust small but powerful travel laptop. I spend a lot of time on the road and on flights, and just got tired of either hauling my 17'' Dell around or using the old 15'' Fujitsu whose battery lasted only a couple of hours. The latter's display finally died, which prompted my quest.
Second, I have several friends who have switched to Macs and plainly drool about them. Most of those tend also to like photography, and Apple seems to be the standard among photographers and graphic artists. While I am not a photographer, I do like tinkering with Photoshop. I also do some simple podcasting and video editing, and was bummed by how few PC programs are available in comparison with Mac ones. The podcasting software I use, Profcast, has a minimalistic interphase for PC compared to the full-blown sophistication of the Apple version. 
Third, I realize that the compatibility issues are not as bad as before. I am still considering if I want to install BootCamp to use Windows 7 in parallel. So far all the programs that I use have their Apple versions. My trusty old Dell has been promoted to home computer in case I get an acute case of PCitis. 
My final reason was my growing reliance on working in the cloud. I have started to write my new documents as google documents instead of Office. That way I keep them online, I may download a version just in case, but can work anywhere from any computer. I use Dropbox to keep my most important files synched to both computers and my Droid. I do not feel encased in the Apple or any other system.
For the record, I had a hard look at iPads and Chromebooks before the decision. I have been wooed by the esthetics of the iPad, but I realized that they lacked many of the functions I needed, not to mention it seems to be a much more closed system. As for Chromebooks, I do need a hard drive as there are programs that I cannot run in the cloud, and some of my files are just too big. 
My new toy, a 13'' MPB with 4 Gb RAM and an i7 processor arrived 2 days ago. I connected to the internet within 5 minutes. I installed Chrome and visited my websites. Then I downloaded a trial for Adobe CS5 and copied my files to the computer. Also downloaded Office and a bunch of other programs that I use, installed Skype, Dropbox, Profcast, and Evernote. As for tonight, I am perfectly set within the boundaries of my computer. Next week, before I leave for a conference, I need to figure out printing and what I need to connect to projectors and the like. 
I hope everything works as well as my wireless keyboard. When I connected the USB gizmo, a message popped up "your device needs to be identified." I sighed, readying myself for a long session of reading instructions and searching for drivers. Instead, I was instructed to press down 2 keys on the keyboard and that was enough to identify it. I sat wide eyed for a while. This was just too easy.
So far so good. 
Update one day later: I connected to the printer...and it printed. Just like that. OMG.

Sunday, May 8, 2011

Virome thoughts after bodyboarding

Since I started reading about the incredible diversity of the microbiome (and trying to keep up at least with those living in and on the human body) I was dreading the coming of the virome. Meaning, the coming of the point where I could no longer blissfully ignore the omnipresence of those pesky organisms, such as I have been ignoring for decades the existence of neutrinos and subatomic particles. It is strange, considering that my postdoc project was all about LCMV, the lymphocytic choriomeningitis virus. But for me it was more a tool, a way to produce the diabetes model where to study the "big boys," the cells of the immune system.

An incredibly informative book came out recently, Metagenomics of the Human Body, with Chapter 4 dedicated to the human virome. I sighed. And read. 
"Whenever microbes (bacteria and archaea) are present, their viruses will be found." Such a simple statement, indeed. But in a way, it is an eye-opener. Of course they will be. We are all connected. Those incredibly intricate webs of parasites within parasites, are just examples of the rule. 
"Compared with environmental viral communities, the diversity of the human virome is low," state Haynes and Rohwer in said chapter. There are only 1500 viral genotypes in a healthy human virome, in contrast to the estimated 10 thousand-1 million genotypes present in 1 kg of marine sediment. 
Somehow that number still haunted me this morning, while trying to catch some of the not-so-great waves at Tourmaline beach. I have had some sinus issues the past weeks but decided that salt water ablutions (even if involuntarily) would do me good by flushing my mucous membranes. Of course I was thinking of the effect on the pesky Streptococci and the like lurking in my throat and nearby. But what about their viruses? And the viruses of the ocean? At the end of the session I was wondering if anybody had compared the microbiome of people who spend time in the ocean regularly with the land-dwellers.
Just for fun ran the search "surfer" and "microbiome" through several databases, no match, of course. Google came back with pages dedicated to surfing scientists. I do have to mention undergrad Amanda Shore. She is studying the effect of zinc on the intestinal microbiota! Why is that interesting for me, because zinc is the only supplement I take, especially when I have infections- it is known to stimulate the immune system. 
But I have gone off-topic. As mentioned before, I need to get more acquainted with the virome. 
I pick up my weekly Science- one of the few that I like to read in paper form, and what the word virophage jumps at me. Ok so those are phages that prey on viruses. The Sputnik virophage, discovered in 2008, is the first example of a satellite virus, which multiplies inside a cell (in this case amoeba) already infected with another (giant) virus. The particular article that I saw was published in PNAS and reports a virophage that by infecting viruses that infect algae, is able to regulate the bloom of the algae in several lakes. 
Another marine article that caught my eye was a recent one in Microbe magazine about coral reefs and their microbes. The coral holobiont, a collection of microbes associated to coral reefs (and yes, there are viruses there also), varies according to seasonal and biogeographic patterns, and can also be influenced by pollution. 
Time to go and rinse my wetsuit...

Thursday, May 5, 2011

Open book exams, redeemed, but left behind

I have an ongoing struggle regarding open book exams. For a long time I did not even consider them. Then, when I started teaching some very intensive, material-heavy classes (such as anatomy/physiology combos), I realized that I could not base the assessment on students' ability to recall details that are necessary in order to do the actual analysis/problem-solving. In real life all of us look up data in electronic databases. So I started trying out open book and/or open note final exams.
I have learned several facts along the way:
1. it is much harder to develop good open book exams. There must be a balance between the different skills evaluated: finding the information quickly, applying the concepts, making deep analyses, and writing in a concise and clear manner. I usually have questions in all ranges, where essay questions demanding analysis and good writing provide the points for an A grade. 
2. One has to avoid answers quickly found through the index. I learned the hard way when in an exam where I asked for an example of structure and function at different levels (tissue, organ etc), the overwhelming majority of the students wrote about the stomach. I was surprised because we had not covered digestive system in that particular class, but students later pointed out that stomach was an example of structure function-relationship provided in the book, which could be found by looking in the index. In a recent exam I asked for examples of homeostatic regulation, and clearly stated which ones could not be used (after carefully perusing the book for clues). 
3. They take time. Closed-book exams take usually between 1-2 hours, maybe more if there are slow/thorough students. For the latest one I had to tell the 4-6 students remaining that it was time to go after 4 hours. Some of them had not even started the essay questions. Those are the times when I wonder about hidden disabilities. 
4. They work. When I finish preparing the open book exams I often think that they are too easy to pass. I include on purpose those more demanding questions for the highest grade, but in my mind there is no way anybody could flunk the exam when the book is available. I am consistently proved wrong. There are students who fail the open book exams. True, they tend to be the weakest students, those who had usually failed the other exams. Or the uninterested ones, who sit in the back behind their laptops and never show up for review sessions. But the fact that they fail even with the material available tells me that they lack basic study skills. And that is a scary thought when it is about students who have been through years of college.
5. They tell me more about the students than any other kind of exam. I learn a lot about my students reading their exams. Some of them write in a sloppy way but showing 'common sense" and experience. They know what the issue is, but have difficulty translating it to the language of science. They cut through the verbiage but miss the chance to show deep understanding. Others look up words and copy paragraphs from the book related to the question, but never really answering it. It is common, but especially disappointing when coming from students who have done "great" in other exams. 
6. They are bygone. More and more students have ebooks instead of "real" books. This time it was only 2 students, and I was able to get them books, but I was aware they were in disadvantage, as they could not use their highlights and notes. On the other hand I could not have them bring their laptops and do word searches (or even sneak into the internet). 
7. Open note it is. I have had open note exams, and they actually feel better in the sense that note preparation itself is a skill, and students learn just by preparing them. However, I have to think ahead really well in setting the parameters of the notes allowed. Also, I will have to actually check if the students comply with those parameters. Policing is not my cup of tea, but in this case it is part of being fair. Ugh.
So it is kind of anticlimactic that after evaluating my latest and in my opinion, so far my best open book exam developed, I decided not to do it again. However, for the next installment of the course I may do an open book quiz early on. That way I could gauge earlier the level of class and identify those students who may need extra attention. Or just to get them know better. 
What are your experiences with open book exams, dear readers?