Rotations...

In reading quite a few books about the history of famous scientist, I've often been struck by the differences between how grad school used to work as compared to how it is now. Grad school was so uncommon at one point that it appears that you had to go out of your way to contact a professor whose research interest coincided with your personal interests. More significantly, you typically already had to have a a project in mind when you decided you wanted to enter a program - or at least some vague idea.

I've always felt that there's a certain appeal to this system. For one, I think that way too many people are going to grad school as the 'next logical step' after an undergrad; it's pretty clear that there's an over abundance of Ph.D.s and not enough jobs. But also, there seems to be a lot of people who simply aren't all that into research (see my previous post on the topic).

Because of this, I have to admit that I've never been a big fan of the 'rotation' system whereby new students apply to grad school in a general fashion and then do 4 months of work in 3 different labs before choosing the one that they find most interesting to complete their degree. I've always felt that this system downweighs the commitment that should be going to grad school (or at least postpones the decision of what to do until you're deep into the system).

All of this being said however, I recently had a discussion about this topic with a grad student who made a very excellent point: a lot of PIs are terrible supervisors. The benefit of the rotation system is that it can be thought of as an extended two-way interview allowing both student and supervisor to evaluate each other's potential for collaborating.

I'd always narrowly looked at the system from the perspective of indecisive grad students, but having been in work situations wherein I was deeply unhappy, I can now see the logic in a reassessment of my previous opinion. I suppose it's always a good idea to reevaluate one's preconceived notions.

Rant: Phones both Smart and Dumb...

One of the great ironies of my life is that despite having grown up the son of the manager of a cellular phone company and having been surrounded by cellular phones since the 80s, for the longest time, I was a personal communication Luddite. I didn't get a cell phone until I was essentially forced to during my M.Sc. (I was away from home ~75% of the time and thus no one could reach me), and even then I opted for the least feature-rich, cheapest model.

I actually stuck to 'dumb phones' until a year ago, when I got aggravated that my previous postdoc wasn't allowing me to check social networking sites1. I was already stuck on a Verizon contract at the time, and therefore had to choose between their Blackberry and Android smartphone offerings. Given that the former's troubles were already quite apparent, I settled for the HTC Droid Incredible™, which had received quite positive reviews as far as I could tell. While I've certainly enjoyed many of the phones functions, I very quickly became familiar with what has affectionately been referred to in some circles as 'Android jank'.

I should mention that before I picked up the smartphone, I'd used my iPod Touch to play music. The 'iTouch' is of course an iPhone sans phone, so I was familiar with Apple's slick user-interface and design. It's difficult to overstate the difference between the 'i' devices' ease-of-use and the wild west that is the Android landscape. Whereas a premium is placed on consistency and elegance in the user interface of the former, every single app controls differently in the latter. In fact, Android apps are annoyingly constantly being updated in order to fix user interface complaints. This frequently requires 're-learning' where all of the buttons are. While it's true that many Android apps theoretically have more options than iTunes Appstore offerings, there's no guarantee that said options will not be located in tedious nested menus navigated by ludicrously small buttons.

Furthermore, there's a lack smooth elegance to the Android interface. Apps frequently have load times, which strikes me as rather insane on a portable device. It's not uncommon that that, while stopped at a red light while biking, I'll want to scrub forward to the next song or podcast in my playlist2. Unfortunately, bringing up the interface to do so takes so much time that I have to put the phone back into its holster before the deed is done. How does that make any sense? Some music programs let you switch songs without 'unlocking' the screen, while others don't - it seems that nothing is consistent in the world of Android3.

Speaking of podcasts, I recently began listening to a rather 'techy' one at tested.com (This is Only a Test), which involves discussions about the latest in gadgets, electronics, and computers. Over the few episodes that I've heard, the staff of Tested have been quite critical of Android as a platform, and one of the big reasons is this:

The original image and description are available at theunderstatement.com, and show that the majority of Android phones are a) released without the most current version of the operating system and b) receive very little if any software update support. This is in comparison to Apple products (shown at the top), which receive the newest versions of their OS as they're released, and continue to have bugs fixed and tweaks made.

The link above spells out a long list of why this is significant, but I'll throw out only two things that matter to me. 1) while some of this Android Jank is getting fixed by the OS manufacturer (Google), there's no guarantee that these fixes will ever be 'pushed' to your phone. 2) It's not surprising that Android apps are so buggy given that developers have to try to support every random version of the OS that still may be floating around out there.  

None of these details have been ruining my life or anything, but they have been annoying. When I got an email about 'upgrading' my phone at a discount, I decided that I wanted to return back to the Apple fold opting for an iPhone 4S. Coupled to my new Macbook pro, I suppose that this puts me firmly in the Applenaut camp, but that doesn't bother me. I only care that the stuff I own gets the job done. We'll see if this does the trick.

1This could be a post in and of itself: Somewhat amazingly, I didn't actually use Facebook until well into my previous postdoc. I'm not exactly sure why, but the benefits of keeping in touch with old friends and colleagues didn't occur to me, I guess. Regardless, one could ask whether being able to check Facebook during the workday really should be a personal goal in the first place. I've come to realize that social media isn't only a forum in which to 'goof off', but also tends to be the modern method by which information is disseminated quickly. I get a lot of my info about science and other important news from Facebook and Twitter, and through experimentation and self-discipline, have tried to minimize their distractive influences.

2Like in Maryland, in the great State of California, it is legal to listen to music in a single ear while biking. I've recently found that an excellent way to do this is to use an inexpensive Bluetooth headset. I recently picked up the Plantronics Marque™ M155™ Bluetooth Headset, which has shockingly good sound quality for listening to podcasts wirelessly while biking.

3A couple more criticisms of the Android platform: Compared to Apple's, the on-screen keyboard is awful (even acknowledging that Android got 'copy/paste' before Apple did). Writing texts or brief emails is a chore and the auto-correct drives me mental. Downloading a ~$3 third-party replacement called Swiftkey helps a bit, but doesn't fix the fundamental touch-screen problems. Finally, the Android's on-device directory structure is maddening, and trying to figure out where to dump music (or where it downloads from the Amazon MP3 store for that matter) is frustrating. Anyone could've figured out that letting every piece of software create its own randomly named directory in the root was a terrible idea. 

Muir Woods...

John Muir (1838 - 1914) was a Scottish-born engineer and naturalist who immigrated to the United States in the mid-19th century and is famous for: a) having successfully petitioned Congress to pass the National Parks Bill (involving the establishment of Yosemite and Sequoia National Parks in 1899), and b) having co-founded the Sierra Club in San Francisco a few years earlier in 1892. When, in 1908, then President Theodore Roosevelt agreed to raise a national monument protecting several hundred acres of old growth redwood (Sequoia sempervirens) rainforest, he agreed with Congressman William Kent that the monument should be named in Muir's honor.

I travelled to Muir Woods National Monument (or simply Muir Woods for short), located in Marin County, a very short drive north of San Francisco across the Golden Gate Bridge, this past weekend to do a little bit of walking under the world's tallest species of trees1:

Regardless of whether the redwoods found in the Muir Woods are the tallest, there's no denying that they are very impressive, stretching out dozens of meters up into the sky (the tallest on record measures ~115 m or 377 ft):

 Without a 'fish eye' lens, it's difficult to capture both the height and the girth of these trees. I remember thinking that trees were much taller on the west coast as compared to the east when I lived in Vancouver, and yet the trees I saw there have nothing on these2.

As night was falling, a friend snapped a photo of yours truly standing under one the the bigger trees. Many of the trunks formed hollow structures that could conceivably be used by someone as a temporary shelter. Perhaps Native Americans did so?

I can understand why the woods themselves are a major a attraction in the area: In addition to being gorgeous and scenic (as well as a short drive from the city), they also make for a rather leisurely stroll. Unlike many 'parks', Muir Woods is quite a flat path and doesn't require any sort of hiking skill or effort.

A visit to the woods is very much a gorgeous nature-stroll.

For anyone who's interested in seeing some more photos from the park (as well as a scenic overlook of Southern Marin County), I've created a Picasa Web Album of the snapshots I took.

I will leave you with one more photo, however. This one is taken from the winding road leading up the mountain that ultimately brings you to the entrace to the woods. The town in the foreground is Sausalito, of macademia nut cookie fame, while the second town across the water is Belvedere. Furthermore, the Bay Bridge, Treasure and Yerba Buena Islands, and the city of Oakland can be seen of in the distance. Sometimes I do wish that I had a fancier camera...

1The actual tallest redwoods are found in Redwood National Park, which is several hours drive north of the SF Bay Area.

2Nevertheless, there is a species of tree found in British Columbia (as well as Washington State and Oregon) called the Douglas Fir (Pseudotsuga menziesii), which is almost as tall as the Redwood, but not quite. 

California Academy of Sciences...

I'm a big fan of Natural History Museums and have been wanting to visit the California Academy of Sciences (CAS) Museum in Golden Gate Park, San Francisco, since moving out here a little over a month ago. I'd actually heard about the reconstruction of the museum a few years ago on a podcast, and was interested in seeing what a modern version of such a place would look like (its present incarnation was completed in 2008). Unexpectedly, I ended up having pretty mixed feelings about the place; so much so that I didn't end up taking all that many pictures. 

I didn't take a picture from the outside because the weather wasn't great, but this pic gives you an idea of how enormous the building is. 

One of the claims associated with the CAS is that it's one of the largest natural history museums in the world. In terms of volume and or floor space, this is entirely possible given that a large proportion of said space is simply open air. It's like being inside a gymnasium with a few exhibits here and there.

It's gorgeous and modern, but there's a lot of empty space in the building, especially compared to other more famous natural history museums such as the American Museum of Natural History (AMNH) in NYC and the Smithsonian National Museum of Natural History in Washington, DC.

Despite the emptiness, there's still quite a few interesting exhibits at the museum, including a rather neat circular walkway climbing up from the flooded base to the canopy of a miniature, climate-controlled rainforest; complete with birds, butterflies, and a host of fish and frogs. Other wings include a penguin cage (which happened to be closed when I was there) and a swamp hosting the museum's 'famous' rare albino alligator:

 Weird isn't it? It looks like someone just painted the thing white.

I remember reading an essay by the late Stephen J. Gould about debates regarding the design of Natural History museums. Essentially, it seemed as though this boiled down to two views: one could arrange the exhibits somewhat haphazardly such that visitors could choose their own order of visitation, or one could try to guide visitors through a coherent 'narrative'. If I recall correctly, Gould favored the latter, with a typical tour going through, for example, early earth geology, then early life, a historically progressive series of fossils, and culminating with the early hominids, for instance. The alternative design, where people wander into whatever room strikes their fancy, is a bit more like the old aphorism about biology being 'stamp-collecting'. I had the impression that the CAS was somewhat haphazard, though I can't be quite sure as some of the exhibits that I wanted to visit were closed off due to 'private functions' (see below).

Ultimately, the quality of message is what matters, and the scientific presentation of the exhibits seemed well-implemented and designed to interest the average attendee. It's not entirely fair for me to be judging a relatively new facility by the standards of facilities that are widely regarded as some of the premier institutions in the world. Nevertheless, there is one real 'kicker': the price of admission is a whopping $301. By comparison, the AMNH in New York has a 'suggested' donation of $16, while the Smithsonian in DC is FREE. This makes the CAS one of the most expensive museums that I've visited despite the one exhibit that I'd specifically wanted to see due to recommendations - the live penguin tank - being closed for the use of a science-educator conference!!!

I'm glad that I visited, but unlike my many trips to the Smithsonian National Museum of Natural History in DC - I'm not sure that I'll be tempted to return to the CAS very soon1 :-(  

1In all fairness to the California Academy of Sciences, given its location in the ultra-touristy city of San Francisco, it's perhaps understandable that they're pursuing the 'theme park' model of admission fees. While a single admission is $30, it's only $99 for a year's membership, which includes unlimited admission to the museum as well as additional privileges for yourself and a guest. Therefore, if you and a friend planned to go more than once per year, the membership would be worth it. Much like many theme-parks, it seems to be gouging tourists while making it attractive for locals to purchase an annual membership.

Back to the Bench...

It's surprising (or perhaps not) how many graduate students I've met who couldn't wait to be finished with school so that they could get the heck out of doing research. I suspect that a significant part of such feelings comes from a disconnect between the expectations of what it will be like to do science based on what one learned in undergrad vs. the unfortunate-but-necessary tedium that underlies the routine practice of experiments. Counting embryos all day for weeks on end, for example, is not a uncommon part of a typical developmental biology project.

In addition to the above, I think that some degree of being turned off from research probably stems simply from doing a project in which one has no interest. I recently attended a lecture by Micheal S. Brown, who shared the Nobel Prize for Medicine and Physiology in 1985 for elucidating the mechanism of cholesterol biosynthesis. The work that he described was both fascinating and inspiring, but also, at least in terms of my interests, very tedious. As was pointed out after the lecture (I'm paraphrasing): that 35 years of work can be represented by one PowerPoint slide with a few arrows on it tells you something about the laboriousness of said work. The routine 'drudgery' of the lab is only bearable if you're doing something you're honestly interested in. 

After over a year of struggling through a lot of work that didn't pique my interest, I'm finally working on some projects that have got me excited. Furthermore, they're in two fields in which I'm personally invested1: the evolution of a) development and  b) gene regulation. The first (side) project involves doing working with some familiar data in Drosophila melanogaster, the organism that I've spent the last ~6 years studying, in order to pursue some of the interests I developed during my Ph.D. On the flip side, the second (main) project requires me to learn about a new model organism group, that of Saccharomyces (including S. cervisea, baker's yeast).

The computational tools that I've used in previous genomic analyses will transfer without difficulty to my new study group, but where I'll have to spend the most time (at least initially) is learning how to work with yeast itself - something I have done in the past while TA labs and such, but never using the kinds of protocols I'll be implementing soon.

Thus I find myself gearing up to begin practicing my mean molecular biology 'bench skillz' once again. I haven't actually been away from the bench for more than 4 months at a time (which is good), but the past couple of years have found me spending more of my average day sitting in front of a PC than ever before (which is bad2). This will soon change, however, as I attempt a grueling, week-long protocol which no one I know has any experience... 

I'm excited though, because, no matter how many times it fails, I still look forward to bench work!

1On top of the two reasons listed above leading to one being turned off of research, it's arguable that being stuck doing something one isn't interested in during a postdoc is even worse. At this point in an academic career, you're supposed to be spending a lot of time developing a research acumen of your own, and it's difficult to see how you could accomplish this effectively by doing something you dislike.

2My current issue with computational work is ergonomics. The majority of lab work-spaces were built long before the age of computers, and thus they're not well suited to long days of typing-away at a keyboard. I'm not tall to begin with, so I find myself sitting in awkward postures in order to reach the surface of my desk. I've been having off-and-on problems with my wrists and my ulnar nerves, which is not a good sign. Thankfully work is providing me with a fix for my desk (a keyboard drawer), but I'm trying to minimize my typing time until it arrives.