The Future is Now...

As mentioned in a previous post, I've been listening to some 'tech' podcasts recently. It on these podcasts that I first heard about 'Siri', the cloud-based voice recognition software that Apple acquired a few years ago and made available in its current incarnation on the iPhone 4S (Apple's official perhaps somewhat idealized advertisement video can be found here). Having been very disappointed with previous voice recognition software1, I didn't really pay much attention to it.

Then I ws biking home from work, listening to some music through my bluetooth headset, and thought I'd give the system a try. My phone sits in a pocket on my biking jacket, and activating Siri requires only holding down the iPhone's 'home' button for a few seconds. I tried a bunch of different ways of saying things, and while I got some odd results at first, I began to figure out things that work consistently.

For example, I can say 'shuffle playlist jogging' and it'll start playing that particular playlist. 'Next song' skips ahead, 'pause/resume music' do just that, etc. You can actually say things like 'Play album Thank You' or 'Play podcast Giant bomb' and it'll actually do it. Furthermore, if I get a notification tone while biking I can say 'Notifications' and it'll read off any new emails, txt messages, tweets, etc. I've received. Maybe I'm easily impressed, but this is pretty Star Trek to me2. Oh, and is there anything better than a lab timer that you can talk to? ('Set timer, 45 minutes').

The one area where Siri isn't so great, at least so far, is in taking dictation. That's not exactly fair - it's quite accurate if you stick to common, well-defined words. However, as a scientist who uses a lot of non-standard verbiage, Siri's not particularly useful; it does incorporate some good ideas though. For one, it highlights all of the words that it detects as ambiguous - this includes both misunderstood words and homonyms. You can then click on them and select from a list of best guesses or edit them yourself. This is not particularly useful as a hands-free feature, though. I can see some utility in being able to fire off quick acknowledgement replies to emails or text messages, but I doubt that many screenplays will be written by dictation.

It's not clear from the Apple website, nor the dreaded Wikipedia how Siri works, but according to the Tested.com podcast, the system actually offloads data-processing to Apple's 'cloud' servers where the heavy crunching is done. The results are then sent back as text to your phone (in practice this takes a matter of seconds)3. If this is the case, it's an interesting glimpse into the future of processing, where your PC will be naught more than a box connected to the internet and the heavy lifting will all be done on servers.

Stuff like this makes me think that current/future generations take technological progress for granted. In our parent's first 30 years of life, they went from what: AM to FM radio? Teletype to fax machine? Mimeograph to photocopier? Frustrating wheels to power steering? I'm exaggerating a bit, but it's difficult to understate that we've gone from the Sears Wishbook of my youth to buying stuff on Amazon.com over 3G Wireless internet on our cell phones, or looking up stuff in a 12 volume encyclopedia to searching libraries of text on Google.

I challenge you to go back and read sci-fi books from the 70s. In much of the imagination of those authors, we're already living hundreds of years into the future4.

1Did anyone ever try Dragon Naturally Speaking back in the day? This was a piece of sofware that would allegedly allow you to dictate Microsoft Word documents. I tried demos of a few versions and remember being stunned by how poorly the software worked - It's not exactly useful if I have to go back and correct the dictation by hand every 5 or 6 words.

2Incidentally, the pocket I use for my phone happens to be on the upper-left side of my chest. Thus activating Siri basically involves me 'tapping' a virtual communicator badge thingie...

3This explanation seems a bit weird as it means that you require an active data connection to tell the phone to play music. It may, however, only do such cloud processing for internet related searches and not for on device lookups. This cloud thing also may explain why the system doesn't work on previous iPhones, even when 'hacked in' - Apple can tell the phone's model when the servers are accessed and thus it can reject the data.

4For instance, in the classic sci-fi book The Mote in God's Eye (1974), the authors, Larry Niven and Jerry Pournelle, predict that by the year 3,000 we'd have invented faster-than-light travel. Yet we'd still lack wireless networking as well as contemporary laptop computers. The sci-fi novels that impress me are the rare ones that really 'nail' it. I'd still rank Neuromancer (1984) among the finest in this tradition, as well as the odd, yet interesting, Snow Crash (1992). This being said, I'm not the most well-versed in classic sci-fi. I'm always looking for recommendations though!

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.

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. 

Stanford...

The reason for the lack of recent updates to the blog is obvious: I just started a new postdoc and am scrambling to get my new projects underway! Don't worry, this busyness is a good thing as it indicates that I'm finally doing something I'm actually interested in studying. I'm sure that I'll have more to say about my research (and what it's like to switch to a new research organism for the third time now) in a future post, but for now I figured that I'd blog a bit about my three weeks of experience working at Stanford.

Leland Stanford Junior University is 'widely considered' to be one of the top research universities in the world (or at least America according to a public Gallup poll where Stanford came second only to Harvard). I can only guess as to how such things are measured, but as far as my new department, Biology, goes, it certainly harbors many well-known and respected researchers.

Now if such a judgement was based on the number and/or density of obvious displays of wealth demonstrated by a university, then I could totally see Stanford being up there. Working around this place is honestly a bit surreal:

 The Stanford campus is absolutely gorgeous, with palm tree lined streets and walkways, fountains at most of the major intersections and meeting places, and beautiful adobe wall and terracotta roof buildings. I've said it multiple times to the agreement of fellow Easterners who have also come here - it's kind of like working on a resort every single day. The only downside, as has been pointed out by Stanford alumni, is that you're pretty much guaranteed to move on to somewhere less attractive, creating a nebulous, 'suckier' future.

Harvard, Stanford, Yale... We just don't have these types of expensive, private universities in Canada. Excluding everything but tuition (room and board, books, etc.), the average yearly cost of an undergraduate degree at Stanford is $38,700 USD1. Thus, it is perhaps not surprising that signs of 'money' are kind-of everywhere here.

I don't want to come off like a yokel or anything, and it's not like I grew up in a poor family, but it's somewhat mind-boggling to me to compare my undergraduate experience with what I can imagine is that of many students here. To give you an idea, I lived in residence at Dalhousie University with my meals covered, and had $20 in 'spending money' per week! Thankfully, most of my peers were in a very similar boat, so I didn't feel excluded (nor did I graduate with crippling, unreasonable student loans).

Stanford is apparently somewhat known for how large and spread-out its campus is. For instance, it's roughly a mile walk from where the commuter train drops you off at the entrace to campus, to the actual location of buildings and residences. So many, many people bike to get around (there are also frequent, free commuter shuttles). Unfortunately, a lot of undergrads cycle rather unsafely - too quickly, or on busy pedestrian sidewalks. That last point actually irks me a lot because almost all of the roads have bike lanes, and many of them are CLOSED TO VEHICLE TRAFFIC. Get off of the sidewalk!2

Scientifically, the facilities are great and the atmosphere of collaboration and comraderie appears to be quite excellent as well. That also extends beyond Stanford itself as UC Berkley, UCSF, UC Santa Cruz, and other universities are also rather close by here in the Bay Area, so there's always opportunity for meetings of minds and such.

This is Stanford's Hoover Tower, named after former president Herbert Hoover, who actually attended Stanford during its opening year (1891). The structure 'towers' above the rest of campus, and provides a much needed reference point for people unfamiliar with the lay of the land. 

Here's a photo of my building, Herrin Labs. This is the front, but on the opposite side of the building, there's a beach volley-ball court surrounded by palm trees (the actual view from our lab).

At this point, Stanford definitely looks like a nice place to work. I've taken a few more photos around campus, so if anyone's interested in taking a look at them, I've put them into a Picasa Web Album: Stanford Campus (Oct 2011). No matter how the research goes, at least I'll be able to say that I enjoy where I work! (Pardon the dark humor, I'm actually quite psyched about the research and have a really good feeling that it's gonna turn out great!)

1Of course, because the university can afford to be so selective about applicants, many students come here with scholarships and at least partial funding.

2As an avid cyclist myself, I find seeing other people being careless about their biking infuriating. Not only is it generally very dangerous, it also creates a bad reputation for cyclists in general. I've only been here a short time, but I've seen some of the most ridiculous biking faux-pas: People crossing perpendicularly through traffic without the right of way at full speed, and even some idiot who was biking on a busy pedestrian sidewalk while texting. The sidewalk thing really drives me absolutely mental.   

First Impressions of Redwood City...

There's always something terrifying about paying a deposit for an apartment that you've only 'seen' online. Descriptions are obviously biased by the renter, and it's tough to get an idea of the surrounding area without visiting. With the exception of the first apartment where I lived during my Ph.D., I've been pretty lucky so far. Thankfully, that trend seems to be continuing here in Redwood City, California.

The new apartment is approximately the same size as my previous one, and appears to be clean and perfectly suitable to my needs and lifestyle. The street immediately adjacent to the new place is a bit odd though, as it appears as though there's some kind of junkyard-thing going on behind one of the buildings. I was worried at first, but then discovered that it's an island of isolated weirdness in what otherwise appears to be a very nice town (all photos are taken from within very close walking distance to my place):

An interesting claim to fame... wonder if it pisses off the libertarians every time they drive beneath the sign? ;-)

Roughly 5 blocks away from my place is the Redwood City Historic District, which is really cool. It's basically a bunch of older buildings (by western North American standards) that are now used as locations for shops, cafes, and restaurants. There's also a really nice gym there with excellent rates ($30/mo). The Stanford gym is free, but with this place being so close, it's arguably much more convenient for me... Tough choices.

Directly off from the historic district is the Theatre District, which features very nicely maintained palm trees flanking more restaurants, pubs, nightclubs, and a large movie theatre.

There are many very nice buildings and interesting things to look at here. Wonder how long before they become 'part of the background'. There's me being cynical again. 

Overall, the city seems to be quite pretty and 'quaint'. I've put some more pictures into a Picasa Web Album for anyone who's interested in seeing more. Everyone I've met has been super-friendly and talkative. There are grocery stores, pharmacies, a 7/11 and a really nice bike shop near me so all is good. I'm also closer to public transit here than I was in Maryland as well, which is great, so things are looking up.  

I'll finish with a couple of observations about California so far: a) Beer, wine, and liquor are cheap and available for purchase at the grocery store. This is convenient, though I hope to not have any reason to 'take advantage' of this bounty. b) It's quite hot here (unseasonably so according to the folks I've spoken to) but nowhere near as humid as Washington D.C., so I think I'll be able to deal.

I begin my new postdoc on Monday, which will give me a few more days to explore the area. Hopefully I'll have more to say about it soon.