A Sober Reflection as I Pass a Milestone...

With the beginning of this month my NSERC PDF will expire, ending my ability to claim that I am bringing 'my own postdoctoral funding' to the table. I figured that this occasion was as good a time as any to reflect on the time that's passed since I completed my Ph.D. in 2009. Anyone who knows me will also know that I'd been generally disappointed with my postdoctoral progress. After what I felt was a very productive and enjoyable Ph.D., I ended up in a position that was completely unsuited to my working style (planned and goal-oriented), and not-conducive to accomplishing my (many) objectives.

It's really the latter that stings the most, because I've had so many people tell me that the ideas that I put together in order to obtain my external funding were great (not to mention that NSERC chose to fund it). However, I never really had the opportunity to work towards those objectives. I became involved in a large collaborative project, which, while interesting in its own right, was rather 'out of my hands' in terms of specific goals and interests. Despite spending a lot of time on the project, I was a 'cog' in a much larger wheel - a very bad position to be in if you're out there trying to make a name for yourself in a competitive field.

I'm not lying when I say that having to write progress reports to NSERC explaining that I hadn't met my goals was a huge hit to my personal pride. At about this time last year, I was in a position where I seriously thought that my best course of action was to abandon all thoughts of pursuing a career in academia. Despite my best efforts, I'd spent 18 months analyzing data for other people, there were no prospects for first author publications on the horizon, and my own project was completely stalled (though I had finished the process of 'protocol development' and could show that the idea would actually work). Unlike my work ethic during my Ph.D., I felt very little motivation to spend long hours in the lab. If this is what post-Ph.D. science was, I didn't want to have anything to do with it - a rather morose thought for someone who'd become as obsessed with science culture as I had.

After a period of serious deliberation involving soul-searching and much solicitation of advice from former colleagues and and advisors, I decided to give postdoc-ing one more try. And so I ended up moving across the country to new institution, bent on working on a new research organism (I've now moved from fish, to flies, to yeast - the next logical step would be dinoflagellates, I guess(?)).

While it was a bit difficult to find my stride again, my sophomore postdoctoral experiences so far have been quite positive. Stanford is an incredible institution, where the caliber of the work is often inspiring1. My work seems to be progressing quite well: I'm writing my first research manuscript in a long while, and I'm thinking of all kinds of interesting avenues to pursue both while here and in the future. Working long hours hasn't been a problem (or a burden, really), which goes to show how much being interested in one's work matters.

In addition to the work, the San Francisco Bay Area is probably the best place that I've lived so far, and even though I've only been here ~7 months, I've already done many great 'extra-curricular' things. The weather is much milder and more conducive to the ice-water flowing through my veins than was Washington, D.C. I'd take the 'not too hot, never too cold' humdrum of Northern California over the awful, hot, humid, Capitol summers any day.

It has been difficult to let go of my disappointment with the past few years, but the seemingly complete 180° turn that my life has taken since moving out West has helped a lot. Though it's often tough to do, if I force myself to look at the positive, I did learn many techniques and protocols during my previous position that I've been able to apply gainfully to my current work. I probably wouldn't be as productive as I am now without that experience under my belt.

While things are looking 'very up', I'm nevertheless not surprised to read about friends abandoning the topsy-turvy, stressful lifestyle of academia for the relative security of industry or elsewhere. I was able to pack my bags and move out west on whim because I didn't have anything 'tying me down', but many people my age don't have that sort of luxury2. The postdoc lifestyle is neither a great place to raise a family, nor to secure one's sanity. But, it does have it's big advantages as well, of course, such as the ability to pursue one's own interests, the freedom to set one's work pace (as long as it's 'frantic' or above), etc. 

With the benefit of a bit of hindsight, I'm glad that I chose to leave my previous position and keep at this science thing. I've got some ideas on the table, some plans for the future and a good thing going. It's a good feeling being able to say that.

1As well as a bit frightening, to be honest. There just aren't many (any, really) Canadian institutions with this kind of money or 'star power'. It's easy to forget that not every lab can produce the kind of work volume that you routinely see here.  

2Well, I had the 'luxury' of moving out here, but that's not to say that it was luxurious. My institutional change happened over a matter of months and was very, very expensive. Given that I didn't have much time to plan for such a large move, it has left me rather penniless. 

Learning it 'Right' the First Time...

A.S. I realize that this is an incorrect use of 'right'. 

During my Ph.D. a few postdocs lamented that they felt as though they didn't have time to sit down and 'learn how to do things properly'. For instance, when you're analyzing data, there are often many ways to accomplish straightforward tasks such as removing redundant entries from a list or concatenating two large tables. Similarly, if you've ever had the opportunity to learn a bit of PERL scripting, you quickly find out that there are often many, many different ways to get the desired results. However, saying that there are many different ways to do something doesn't mean that all ways are equally as efficient. I had a pretty shocking realization of this a couple of years ago when changing a few lines of a script altered its run time from overnight to ~5 mins (I learned about hashes).

Changing the time it took to generate some data from 8-10 hours to 5 mins was a massive gain in efficiency. Instead of taking several days to get results, I could process my whole dataset in a morning. In fact, even if it took me a whole day of searching, reading, and trial-and-error to learn how to boost my efficiency, it would probably still have been a net benefit.

Yet, most of the time, I find myself in the same mindset as the postdocs referenced at the beginning of this post - it's easier to just trudge through these data (or this protocol) using the techniques that I know rather than sit down and 'waste time' to look up a more efficient method1. Despite realizing that learning how to do something correctly now will reap future efficiency rewards I nevertheless offset future gains due to present circumstances (always pressing myself to 'get more done').

I suppose that it's a small comfort that this phenomenon has been quite well-studied in both psychology and economics under the general framework of intertemporal choice. In general, people have a tendency to perform what is called 'delay discounting', or to discount (often sharply) the value of long term rewards once they pass some arbitrary time threshold (e.g., would you choose between receiving $100 today or $110 in a month?).

Such 'bias for the present' (see this press release for an example), is logical under many circumstances as the future is uncertain. It doesn't really make sense in my case because I've seen the work put into learning some new aspect of PERL, or R, or Linux (or any number of things) pay off time and time again.

I've resolved to be more judicious in my allocation of time towards improving my skills in areas where such improvement would benefit my work. One way to offset the present 'cost' of such self-instruction is to invest more of what would otherwise be 'free time' into it - this may be a good way to offset the 'guilt' of not feeling like I'm 'wasting time learning'.

I am in a field where learning is perpetual, so don't get the wrong idea. What's important to keep in mind is that it often pays off to learn how to do something properly (read efficiently) from the get-go.

1In my experience it's often obvious that there's a better way to do whatever it is I'm doing. When you're developing a new protocol or method, you're typically well aware that you're breaking new ground. Otherwise, there's nothing new under the sun.

Thoughts on the Utility of Seminars...

Everyone who's involved in academia probably has some angst about seminars. At the very least, it's always difficult to figure out which talks to attend when you feel like you already don't have enough time to take care of the work that you have to do. I've seen quite a few seminars at this point, and as the years have gone by, I think I've become more conflicted about them than ever.

I think that there are obviously many 'purposes' behind seminars. For instance, an invited speaker from another institution can tell you about interesting work that, if not directly relevant to your own projects, could at the very least be 'inspirational'. Regardless of whether you're happy with attending seminars for interest's sake (I've done it many times myself and would encourage it whenever possible), I think that there is a way that many of these talks could be made far more likely to be helpful. I also think that this is where my conflict regarding seminars lies:

I don't understand academic seminars that are primarily focused on 'results' rather than methods. Of course we're all excited about telling people about interesting new results, but on top of being fundamental to the practice of science, I think it's often more interesting to learn how those results were obtained.

Some people are probably reading this thinking that I'm crazy: of course people tell you how they obtained their results! While in some fields I think that this is true, I've been surprised by how often in large, complex dataset genomics, people gloss over the important details of analyses. In fact, often people will give the most cursory statement about how a figure was produced, ignoring complicating factors such as which subset of a larger dataset is actually being shown. 

I'm most shocked by presentations of a genre that I've affectionately come to label the 'dump truck' method of presentation. This is the situation where someone plasters each slide with an extremely complex, poorly-labelled figure and basically asks you to take their word for the fact that it's revealing some amazingly novel aspect of biology. The few times that I've seen extremely egregious versions of this form of talk, the only thing that ran through my head was that the speaker really wanted to convince us that they were doing an amazing amount of work... somehow1.

Perhaps I'm naïve or simply missing something fundamental about how seminars 'work', but I get far more out of talks that are as much about how something was determined rather as they are about what was determined in the first place. This is particularly true in the case of 'informal' seminar series, such as meetings among labs interested in the same topic. In many results-focused seminars, I'd rather that the speaker had presented half of the 'neato' things they'd done, if it meant getting a better picture of how such things were done.

Remember, nullius in verba.

1I've received the advice from a few people that this is a particularly bad way to approach a job talk - yet I've seen in done a few times now.

Picnics with Smelly Hipsters...

If you're ever visiting the city of San Francisco, I'd recommend taking a walk through Mission-Dolores Park, located between the Mission and Castro districts (a short walk from the 24th- or 16th & Mission BART stations).

I first visited the area when I arrived last fall and immediately noticed the beautiful views of the city (the park is located on a hill above the downtown area). However, it was rather chilly and the place was pretty empty. Things were quite different there last weekend when the weather was gorgeous and the place was packed... with smelly hipsters.

I hope you're able to see just how many people there are in this half of the park. There wasn't an event or anything - this is just how it is. The only reason that the center areas aren't packed with people is that they're fenced off so that folks can use them to play sports.

Now the Mission District is technically the hipster zone of SF, so it's probably no big surprise that they'd be congregating in the park. But the heavy clouds of marijuana and cans of Pabst Blue Ribbon1 interfere with the relaxation of picnic-ing. 

In all seriousness, I've got nothing against hipsters - except the one's who are actively trying to 'be nonconformist together' (if you get my meaning) - and in fact, there were a lot of strange people of all ilks in the park. For instance, there were people walking up to each group of park goers selling 'magic cookies' or cold beer, both of which are illegal in the park (the former also being illegal everywhere, of course).

Here's a shot looking North towards the less densely packed sporting area. There's a group of young guys playing bocce - a fine sport!

There was also an activity going on that I've never, ever associated with public parks: tightrope walking. Apparently, when you're in a place with palm trees, it's common for people to tie ropes between these trees and make fools of themselves trying to perform circus acts. One guy was really talented, I'll admit, but the rest of it was just sorta weird.

Anyways, as usual I've made a Picasa Web Album with a few photos snapped with my iPhone. A park's a park, so there isn't exactly a ton of scenery to write home about. Next time I'll do a better job of photographing weirdos.

1This is not a stereotype, hipsters actually do drink PBR.

Soft- vs. Hard(ware)...

I've now been a Mac user for 3 years. Before buying in to the Apple camp, I used Linux for computational work and Windows at home. My experiences with Apple products had typically been negative (why can't I properly maximize my windows?!?!?!?), and I had a philosophical opposition to their 'closed' ecosystem1. Then one day, based partially on the recommendations of co-workers, but also on somewhat of a whim, I bought a MacBook and became an Apple fan.

I still have a PC for playing the occasional, umm... videogame, but all of my work and most of my 'productivity' applications (such as writing this blog post) are done on my Mac. The reason is simple: I really enjoy using Apple's software. What all of my Mac-hating, Windows-using friends have always referred to as 'dumbed-down' interfaces, I now see as intuitive. There's a certain elegance and consistency of design among software on the Mac, such that you can immediately figure out how to do things on an application that you've never used before. As an example, take these screen grabs from two relatively similar pieces of software:

The first program is Apple's iPhoto.

The second is Google's Picasa 3.

Just looking at these two screen grabs, it's pretty clear to me that iPhoto is more sparse: There's less clutter on the screen, fewer information boxes, and fewer buttons sliders and toggles. Picasa has more functionality, but (and all of this is just my opinion, of course) that functionality is realized by continuously bolting more features (i.e., buttons and sliders) on top of an already clunky interface. iPhoto is also arguably more 'aesthetically pleasing', but again that's (common) personal opinion. 

There are arguments for both views - Shiny interfaces are often undesirable when functionality is at a premium, after all. But I think that this specific example illustrates a larger problem: why is there so often a disconnect between the quality of the hardware we use as compared to the software running it? Or, for that matter, why do companies that produce very functional software (Picasa) often put little stock into developing their user exprience and aesthetics?

Another example: I got an HP printer-scanner combo thing last year with my new laptop and while it scans great images, the software that came with it is ABYSMAL. There are freeware programs that are so much better. You could repeat this example ad nauseum with various products that have come out over the years: digital cameras, cell phones, MP3 players, etc. Why does their in-box software suck so badly2?

Part of Apple's recent success is undoubtedly due to their concerted effort to improve both the quality of their hardware and their software. This is particularly evident on iOS devices, where the ecosystem encourages uniformity of design such that even very different apps 'feel' the same.

So I guess the real question comes down to that philosophical opposition discussed at the beginning of this post: 'freedom' seems intuitively better in some moral sense, but what if the 'walled garden' approach actually produces better and more stable systems? I'd rather have both options available, but now that computing is mainstream rather than the domain of basement-dwelling nerds, is expecting everyone to 'figure every new program out' reasonable? Can Apple be thought of as simply setting 'standards', something that can enhance a market in situations where too much competition leads to consumer confusion? 

1It's debatable how closed the ecosystem of software has been on the Mac/Macbook side in the past, but it's become more closed with the inclusion of the App store on desktops. The new version of the OS coming out this year may close it off a bit more. On the mobile side (iPhone/iPad), the ecosystem is pretty much as closed as can be: You can't install anything not authorized by Apple without hacking the device. 

2We can always say that these are often hardware companies and that software is a secondary consideration, I suppose. But someone, somewhere must've looked at some of these programs and asked 'are you serious?' The software for my old Sony mini-disc player felt like it had been made in a high-school programing course.