Fastest rejection letter ever.

It’s a little early for me to be looking for a job – I’m still working on my thesis and clearly won’t be done before the fall, but hey, it doesn’t hurt to be prepared, right?

So, last night I came across a job posting on Linked in, posted by a “Staffing Consultant”, looking for a scientist for a big company in the states.  They want 6 years of next-gen sequencing experience (despite the fact the field is only 4 years old), and someone with previous experience in a management role.  I thought 4 years of next gen sequencing experience might be close enough and I do have management experience from before returning to school – so hey, why not apply, right?

Unfortunately, my ego might disagree after getting a quick reply.  (By quick, I mean less than 12 hours, which is a pretty impressive turnaround time for any job application.) The reply, however, was somewhat harsh.  I’ve paraphrased it, but this is the gist:

“Thanks for applying for this position.  We’re only looking at candidates with a PhD, work experience and management experience. We have a bunch of Post-doc positions on our web page – you should check them out and apply for something that fits your current level of expertise/education.”


On that note, perhaps I was a bit ambitious, but hey, nothing ventured, nothing gained.  (-:

ridiculous email.

Sometimes it’s fun to write ridiculous emails:

Good morning 1st floor!

You may notice that *all* items in both of the fridges and the freezer have been marked with a yellow sticky piece of paper. This yellow mark symbolizes your refrigerated item’s impending doom.

If there is anything in the freezer that still has this mark on it by Thursday afternoon, it will be sacrificed to the gods of bioinformatics in the hopes of better results and faster processing times for the GSC. (The sacrifice may or may not involve diabolical rituals and a RIP talk.)

Fortunately for your refrigerated items, they may be spared simply by removing the yellow tag.

Unlike last year, I will not be lenient in sparing “fresh looking” items with the yellow tag… as I found some yellow tags from last year in the freezer. (anyone want a frozen dinner?)

With humour,


I have to admit, I’ve never threatened doom on slightly chilled and expired food items before.  Thursday afternoon should be rather entertaining, I would think.

Way off topic – using nature inspired technology

I saw this video via this afternoon.   Normally, I just listen to this stuff as background noise, but it really captured my attention, and consequently I blew 15 minutes listening to the talk.

It’s described as follows on the TED website: “Michael Pawlyn takes cues from nature to make new, sustainable architectural environments.”  However, it’s also about closing the loop in design, reversing desertification and building a better planet.  If you’ve got 15 minutes, I suggest watching it.

The small things that matter…

I’m sure you can take that title in many different ways, but I have a specific thought in mind – which is probably not what you expect.  And yes, it does eventually come back to science.

About a year and a half ago, the Genome Sciences Centre renovated its lunch room and took out the ping pong table.  Having lost my best procrastination tool, and probably most of the exercise I was getting, I decided it was time to return to fencing, which I’d done in high school and my first year of undergrad.  There’s a fencing club about a 10 minute walk from my house, which makes it pretty convenient too.

After about a year of participating in the intermediate classes on Mondays, I’ve now started going to the free fencing sessions on Thursday.  What’s immediately obvious is that there are two groups of fencers – generally those that are young (<20 years old) and have been fencing for probably less than 5 years, most of whom show up on Mondays, and the older group, most of whom have been fencing more than a decade or two and clearly don’t need lessons anymore. I usually do reasonably well against the younger group – and I’m absolutely slaughtered by the older group.  No surprise.  The older fencers have better technique and that will always win against speed and agility.

In my first match last night, I was devastated 5-1 by a guy who offers private lessons.  No big surprise really, but, in sheer frustration, I stepped back and spent a few minutes watching him in his next match.  Superficially, we do the same things, but upon careful observation I noticed that the biggest difference was simply that he held his blade 15 cm lower, covering his lower body more efficiently.  That’s it.  Just a tiny change in how you stand.

With nothing to lose, I switched my position to mirror his and immediately went from outright losing my matches with the older group to tying them.  I even saw frustration on my opponents faces now and then…. and I held the Monday evening instructor, who always wins against me without breaking a sweat, to a draw. (Normally you don’t draw in fencing, but the wire in my blade broke when we were tied at 4.  Good enough for me!) All in all, I’m thrilled with the change – and have fewer poke marks to show for it today!

Of course, I frequently use fencing as a metaphore for science, so I’ve been thinking an awful lot about mentors and having good examples to follow today – and how that fits into my future career.  I’ve been incredibly fortunate to be thrust into an environment where I’m surrounded by people who excel at their field.  Now, I think it’s up to me to watch and learn.

For me, this translates into a question of what guidance I’m missing.  The process of writing and planning papers is always done behind closed doors and is hard to watch – and is something I would really benefit from being seeing how other people do it.  When it comes to thesis writing, or application notes, I’ve got a few under my belt, but for some reason, I find papers more daunting.

To get to my point, All of this had me wondering what other small details graduate students are missing.  What are the tiny details that you’ve discovered that can make all the difference in getting things done right?

Evening Festivities or being snarky about pac bio’s movie.

Possibly the most exciting thing that’s happened in the past hour is the fact I’ve won a million pounds in a lottery that I don’t remember entering…. although really, I don’t think I’m going to send my personal information to the lottery corporation – after all, the lottery was sponsored by the British tobaco promo.

More to the point, I was underwhelmed by “The New Biology” film shown by Pac Bio. That’s not to say it was bad, but that they’d picked the wrong audience. Really, it might have been good if you were, say, a complete newbie in the field of next-gen sequencing, or if you like snazzy graphics that don’t tell you much. (Yes, I’m being snarky… but I’ve been good all day, so here it goes.)

Personally, I found myself trying to read the lines of perl code that would scroll by periodically in batches of random numbers. I did catch the line:

while (1) {

which has me worrying about the origin of the code and where it came from. (This is one of those things that good coders just don’t do.) I got a copy of the video so I’ll try to figure this out later. My guess is it wasn’t pac bio’s code. I think much more highly of them than that, and this movie was really not designed for an audience of bioinformaticians. I hope the biologists in the audience got more out of it.

I’m also a little wary of the “new biology” paradigm, which was alternately defined as personalized medicine, drug screening, network biology and next generation sequencing. They can’t ALL be new biology… can they? Or did I miss the memo that everything in the future is new biology… hrm.

I suppose It also didn’t help that there were a lot of facebook analogies in the introduction… I’m rather anti-facebook because of it’s policies, and really, I think my database of a billion rows of search-able variations across 2000 samples faces entirely different challenges than the mechanisms used when my nephew tells all of his friends about how much he hates math class… Don’t get me wrong – I love social networking in the abstract, but facebook isn’t my device of choice….and then there was the Monsanto thing, but lets not get into that.

Anyhow, I guess I can say the movie wasn’t to my taste, unfortunately. I can see it doing well as a one hour TV special on the national geographic channel – or even uploaded to youtube, where I’m sure it would quickly accrue several million hits, but my further viewing pleasure will all be with an eye to figuring out where the code came from… or possibly as a drinking game. (A shot every time someone says “new biology” might work well.) Bottoms up!

Ah, Pac Bio, I was hoping for more snazzy technology this year, rather than a disney-esque version of the future. But that’s ok, you’re still my favorite technology… Long live single molecule sequencing!

Ode to Expedited Delay

28 hours after my new laptop was supposed to have left china, it turns out it’s still there – and has left again! I’m not sure how many times it has to leave, but it certainly was unexpected to me to see it sit in china that long after UPS claimed it had left.

In any case, to tide you over till I have something else to write (and to keep myself from hitting refresh on the UPS screen another 1000 times) I thought I’d provide a fantastic “video” of Beethoven’s 9th symphony, 2nd movement. I often listen to classical music while working, but this visualisation is so compelling, I’ve been unable to drag myself away from it. It’s very different than most other pieces I’ve seen visualised in this manner, which is just another way that you can see Beethoven’s genius in action. If you’d like to see other videos, the same user has a whole bunch of them posted – and apparently sells them as videos for $1 each.

Actually, it’s given me a few genome visualisation ideas as well – but I’ll talk more about that soon. I need to finish the revisions for my paper first. Then I’ll talk about what I worked on over the holidays, which might be a good starting point for some future work. whee!

the circle of life..

When I was getting close to the end of my masters degree, a fellow graduate student pulled me aside and asked me if I could think of any algorithms for a quantum computer… That turned into a rather successful biotechnology company here in Vancouver. As far as I was concerned, the quantum computer never materialised – but I don’t think they were necessary for that company. It would have been a nice touch, but it was never a core part of the strategy.

Now, as I near the end of my PhD, my supervisor asked me the same question today. Unfortunately, I’m still not sure that there’s a good answer to it either. I can think of great things I’d like to do with a quantum computer, but I still face the same problems as the first time around:

A) Does it actually exist?
B) When will it be ready?
and C) what can it do?

Coming up with problems is easy – coming up with problems that take advantage of an imaginary computer with imaginary strengths (of which I know very little) is hard.

Somehow, I don’t see this leading to a chapter in my theis. At least, this time, I don’t think I’ll lead to a start up company.

Today’s Music of the Day – Carmina Burana

Another one of my favorite pieces in the classical style is Carmina Burana. It has a neat history, with the texts having been found in a monastery and later put to music by Carl Orf. One of the most popular parts of the music is the “O Fortuna” piece, frequently used in movies that want a medieval sounding theme.

One of my favourite musical passages of all time is at 40:12 in this video, the “In taberna quando sumus”. It’s an incredibly odd piece of music, but just works somehow.

Some mid-afternoon Beethoven

I love classical music – and Beethoven’s 9th has always been one of my favourites – so, I figured I should share the video I’m enjoying at the moment. To get to the Beethoven part of the performance, you need to get past an organ concerto – which isn’t half bad either.

I find the whole concert a little less smooth than I’m used to from other recordings, but it still comes off pretty well. I should warn you that the whole concert is an hour and a half long.

If you want to skip to the good part, my favourite movement is the “molto vivace”, which starts at 30:20.