A Return to Form...

A long time ago in a graduate school far far away I used to loved immersing myself in science. Of course everyone is somewhat immersed in the vagaries of the particular projects in which they're involved, but I'm talking about much more than that; I mean thinking, reading, and talking about the broader themes of science. Where is the field going? What is the relationship between science and society? What is the role of individual scientists in the face of widespread superstition? You know, things like that. I read a ton of random science books and blogged regularly - in fact, some of the major themes of my Ph.D. research came out of random details that I read in older books that got me thinking about their modern applications.

Recently, I've been having more of those sorts of moments again. Conversations with fellow postdocs about subjects outside of the daily grind, big-picture speculations, even random pie-in-the-sky conversations about what we would do if we ever had our own labs. These moments may seem minor when you read about them now, but I must admit that they've had the effect of kindling a long-dormant 'fire' in my 'soul'1. I mean, think about any scientific research project: You spend a lot of time working away at answering a question, expecting that all of your work will eventually pay off. Some of these projects take years, and the way to keep the excitement up is to visualize the end goal. Can't it be the same on larger scales?

There's something to be said about appreciating journeys and not destinations, but ultimately there has to be a destination or else there can't really be a journey, can there? At that point it seems like just aimless wandering, and I think that I'm getting too old for that...

1My metaphorical 'soul' that is.   

The 'lost month' and a big change...

Apologies for the lack of updates around here lately, but in all honesty, the past few months have been some of the most difficult periods I've had in recent memory. It's unlikely that anyone would argue that postdocing isn't a tough business. Many of the postdocs that I know tend to work hours that probably stretch the limit of what reasonable people would consider having any kind of life beyond work. Consequently when, as a postdoc, I say that I've been busy, I mean that I've been really busy.

The major cause of my busyness is that I agreed to contribute a short chapter to an upcoming collected volume on various evolutionary topics. It's obviously an excellent career-building opportunity as well as a chance to produce a professional piece of writing as a sole author. However, it was not part of my 'primary research', so I worked on it during my free time. I'm a little worried that given little time I've had to devote to it lately, it's not going to be up to my typical standards. At least I'll get some reviewer feedback along with the opportunity to make modifications before the final copy goes through.

Another component to my general busyness is a bit more major: After two years of working my ass off, I've decided to leave my current postdoc and continue my career-building elsewhere. Obviously the specific details as to why I've come to my decision are best kept between myself, my PI, and potential future employers, but I can say that this decision wasn't reached lightly. I struggled with whether my current lab was suiting my objectives, and after much deliberation and discussion, I came to the conclusion that it was not. This is a really tough, often stressful, and underpaid job - the absolute minimum one can expect is to actually enjoy what you're doing.

Thus, I am now on the market for a new position. 

One of the major 'stressors' for me in terms of reaching this decision had to do with the strange predicament in which we postdocs find ourselves. There are many of us, many of which are very, very talented. Every time there's an opening for an academic position somewhere, the number of applicants can often be staggering. It's tough enough to compete for a job in the field without the stain of having left a postdoc - especially while you were externally funded.

Honestly, I was so discouraged by the situation that I figured that my only recourse would be to 'bow out' of academia and look for a career in industry. There's nothing wrong with working in industry, of course, but I'd be lying if I said that my dream wasn't to have my own lab some day. Thankfully(?) some encouragement from former mentors and advisors have led me to believe that my chances at having a successful career have not been obliterated by this unfortunate event. My only hope is that I leave my lab on amicable terms, which seems to be the case, for which I'm grateful. 

Oh well, I'm extremely excited by the prospect of moving to a new lab where I can work on a project of my own in a field that I love so stay tuned1.

1My plan is to keep up with regular blogging moving forward, no matter what the future holds!

P.S. As a sign, I saw an awesome 'double rainbow' last week: Perhaps fate (which I don't believe in) is telling me to 'hang in there!'

Wherein I Murder a Little Bit of my Soul, for Convenience's Sake...

I have never been referred to as a Luddite (at least not to my face), as I am somewhat of a technophile (I bought my first HDTV in 2005, for instance). However, there has been one area in which I've been fairly reticent: digital distribution. I guess that the idea of not actually owning what I buy is disconcerting to me. If I buy a digital copy of a movie on iTunes, for example, will I still be able to watch it in 5 years? What about 10 years? Also, who wants to watch movies on their computers (or even worse, their cell phones) anyways? I generally have the same feelings about digital music purchases - data are ephemeral, but I'm not going to lose CDs unless they burn in a fire.

Of course, as they say, all good thing must come to an end, and eventually convenience wins out against unidentified fears. CD cases are awful, being bulky as hell and more fragile than Fabergé eggs. So the cases went the way of the dodo the second time I moved across the continent (the first time is when I learned how bulky they were). Then the world went all iPod and suddenly CDs themselves seemed like a massive waste of space - so I reluctantly went digital.

Digital music, digital videos (Netflix), digital games... There was one holdout though: I LOVE the smell of paper, the feel of the page, the heft of a book, the cripness of a an unworn spine, the subtle roughness of hardcover, the... well you get the idea:

   Few things in life can match the smell of my original American 6th Ed. of The Origin of the Species (circa 1879).

Though I love all of my books as I would my own children, they do present somewhat of a problem, which can be illustrated as follows:

It is decidedly 'not easy' to haul around ~600 books every time one moves to a new place. When I moved from Vancouver, BC, to Toronto, ON, it cost me hundreds of dollars to ship these things by UPS.

The future is uncertain, and I never know where I'll end up next. It would be a massive pain to ship these books, say overseas. And so, the last of my will crumbled and I 'splurged' on a Kindle (the 6" one with Wi-Fi1).

The device itself is pretty good in terms of reading ergonomics, the screen having only slightly less contrast than standard book paper. Also, it can be read one-handed, which is an absolute MUST on DC transit. It has a lot of features that I really appreciate, such as being able to highlight text which is automatically dumped into a text file for quote mining, and being able to add notes and annotations with the small keyboard. I'm not a huge fan of the button layout though, as my massive sausage fingers seem to hit the 'back' and 'menu' buttons continuously while trying to navigate the device.  

The future appears to be lonely.

I looked into the Kindle store and found that a surprising number of the titles on my wishlist were already available in digital editions, typically for $9.99, which is good. Furthermore, and I realize that this will only appeal to a few weirdos like myself, pretty much everything public domain is free - and I'd personally much rather read Plato's Republic on a Kindle than via a text file on my PC.

I have to admit that there's at least one potential, massive benefit to the device in my eyes: There's no reason for any 'ebook' to ever go out of print. As someone who regularly tries to go back and read classic works of science and history, this has been a constant thorn in my side. Many old books either aren't being published or are being sold by specialty publishers at exorbitant fees. I'll gladly pay a reasonable fee for server maintenance and distribution costs to have access to classic works like RA Fisher's The Genetical Theory of Natural Selection (not on Kindle yet). Oh well, it's a brave new world ($6.29 on Kindle) I guess, and we'll see how I feel about it in a few weeks or months. Yes, I am now one of those people. 

1 The 3G Kindle is $50 more ($189 instead of $139). Call me crazy, but I cannot possibly think of a situation where I'd desperately want to buy a new book, but not be in range of a free Wi-Fi hotspot. Well, that is, except for work. They are very anti-wi-fi at work :-(

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Update 11.04.19:

Dear Huxley, I just realized that I typed that I moved from Vancouver, BC, to Toronto, ON, when I actually moved to Hamilton, ON. I've become so used to saying that I moved to DC from 'near Toronto' that I've also become one of those people - The ones from Ontario that all claim that they're from Toronto no matter how far away from the city they grew up.

Getting Old...

I believe that there comes a point in every young man's life, where he realizes that he's turning into his dad (and since my dad reads my blog, I hope he understands that I mean no offence!). You know what I mean: That point in your life where you look at some trend or aspect of the world, scratch your head, and admit that you just don't 'get it'. Consider the following: I found myself in need of some new pants, so I went to the store and tried on some jeans. I found a pair whose fit I liked and bought them... despite their being covered in holes:

This brand new pair of pants has been pre-torn, I can only guess to simulate that 'lived-in' feel?

Is this is what we've come to as a society? A people so lazy that we can't even be bothered to wear out our clothing through regular use? Where we fool each other into thinking that we actually bother to get dressed in the morning by buying pre-worn clothing? Or perhaps the clothing manufacturers have simply figured out a way to remove the middle man in the whole 'planned obsolescence' thing. There's nothing 'planned' about this: My new pants are already obsolete given that you typically buy new clothes once you get holes in the old ones.

I suppose that I am curious about one aspect of the whole pre-worn clothing phenomenon. Do clothes that are pre-worn dergrade more rapidly than those that are not? Or perhaps having already been imbued with holes, it makes it less likely that you'll notice new ones? Methinks there's the makings of an experiment here - something to give to an undergrad or something. I'd better write this down.

Computers in Science...

If all goes according to plan, I will be co-teaching a class this fall structured around topics in the analysis of genomes (genomics, transcriptomics, proteomics, and much more!). This will be part of a new 'section' or department of the small educational wing of our institution, focusing on genomics and bioinformatics - a field in which many people are apparently quite keen on gaining more experience. Interestingly, I was having a conversation with the organizer of this new section, and he told me that one of the core principles that he wants to convey with these new classes is an appreciation for the utility as well as practical challenges associated with computational biology (I'm paraphrasing of course).

If it were up to me, familiarity with Linux, PERL/Python, and R would be part of required classes for any honors major in the life sciences (and I'm sure that it would be useful in other sciences as well). We're quickly reaching a point where the ability to manipulate large datasets is unavoidable. Some labs cope with lack of such knowledge by hiring dedicated statisticians or computational research associates; but such an option isn't always available. Personally, I don't even like this route because it forces you to rely on someone else's knowledge (and potential to make mistakes) in order to interpret your own data. If this is unavoidable, then at least you should be very clear in terms of expectations of your ability to understand what was done1.

The sad fact of the matter is that the folks that I've met who are completely unfamiliar with computational work are sometimes either a) intimidated by it, and thus aren't particularly interested in learning about it, or b) overconfident in what computers can actually do. More troublesome is typically the latter, because it can lead to all kinds of mess. For instance, I once heard about a group of researchers that had generated a very large and very comprehensive dataset for a genome-wide association study of an interesting disease. They had assumed that they could analyze their data using their personal desktop computers, and thus had not left any room in their budget to purchase the sort of high-end clusters (or access to such computing power) that actually required to process such immense data.

As one of my former supervisory committee members was fond of saying: There are more possible alignments of 2 300 nucleotide DNA sequences than there are elementary particles in the known universe. Even modestly sized datasets (I realize that 'modest' is subjective) can take weeks to analyze on high-end desktop PCs. People who work with this kind of stuff day in and day out use much more powerful clusters of processors, designed for this type of work.

It's also important to keep in mind that a computer can only do what you tell it to do: Hence the famous garbage in/garbage out principle. If you cannot conceptualize the solution to a complex problem no amount of computational power is going to be able to provide said solution. At first glance, this appears laughably obvious - but unfortunately, it comes up more often than many of us would like to admit. I don't know how many times I've seen people generate huge datasets of say, expression data, and then expect a computer to find 'interesting patterns' in said data. 

Like any other science, computational biology is still about testing hypotheses. Computers are allowing us to test hypotheses that were previously out of reach, but they do not obviate the need to follow the scientific method.

1Collaboration is both a necessary and desired part of science - pooling together multiple minds of different backgrounds in tackling a project is almost always useful. However, I think it's important to keep a very clear picture in mind that collaboration should not be an assembly line: each participant should be reasonably familiar with all parts of the process. Nullius in verba!

Image cred here.