My sister-in-law got me a puzzle of the day desk calendar for Christmas. She apologised for not giving me something “better” (i.e. more expensive), but in all honesty it was one of the best presents I got this year.

The puzzles from January 29-31 consist of (vaguely) science-related anagrams. In each case, you have to fill in the blanks with two words that are anagrams of each other. The first few were ridiculously easy, but a couple of them proved tricky enough that I had to write the letters of some likely words down in random order to play with.

Who wants to play?!

Only one answer per commenter per hour, please, to give people in other time zones a chance to take part! No need to go in the right order though. I’ll do my best to add answers and bragging rights credit as the comments come in!

1) DNA AND RNA are blueprints for making proteins (Elizabeth)

2) Of all the elements, NONE is as useful for making brightly lit signs as NEON (Alyssa)

3) The coral REEF was FREE of pollution (Kristi. Oh, if only this was true)

4) Because the telescope was out of focus, the astronomer was UNABLE to see the NEBULA clearly (Graham. For shame, Alyssa, for shame!)

5) The brilliant BRAINY scientist could count in BINARY as well as decimal (Ken)

6) When doctors DILATE a patient’s eyes, they see more DETAIL in the retina (Kristi)

7) The computer used a fast ALGORITHM to compute the LOGARITHM of a number (Joanna)

8) You can turn a TRIANGLE into a square by ALTERING the number of sides (Kristi)

9) The doctor had to CALIBRATE his tools to look for a BACTERIAL infection (Stephen)

Have fun!

On the day The Lancet finally retracted Andrew Wakefield’s vaccines / autism paper (six years after most of the co-authors), Facebook’s word capture feature decided to remind me of the importance of vaccination:

Excellent timing, Facebook!

Does anyone have any experience with this organisation? Their website front page states that they are a not-for-profit organisation that is “helping leading researchers in all fields with their non science duties and responsibilities” (emphasis theirs). I’ve somehow ended up on their mailing list, and get frequent emails with an advice column-style question and answer of the day. Some of it has been really good stuff, covering issues such as personnel and laboratory management. You know, the kinds of things that PIs are expected to know how to do despite never being offered any training.

Last week I was offered the chance to download a sample issue of the monthly newsletter, which usually costs $199 (members) or $267 (non-members) for 12 issues. The content was relevant and interesting, with some overlap with parts of my job description. It’s a US publication, with a US-centric content, but most of the articles were more or less applicable to other countries. However, the majority of the articles were very similar to the posts I can read for free on the various Prof-blogs out there.

Does anyone have a subscription? Is it worth the money? Or is it aimed more at PIs who aren’t familiar with the blogosphere?

(Realises that if the latter option is true, she’s asking the wrong crowd. Decides to cross-post on her other blog to increase the chances of finding a blogosphere-savvy PI with a subscription).

Here’s a photo of my best scar, which looks like a winky smiley face. Story here ¹. please leave a caption, or a photo of your own scar, in the comments!

¹ I recycle my blog material for the good of the environment

A number of “my” PIs are trying to develop novel predictive and prognostic biomarkers specific to different tumour subtypes. We have excellent resources for this kind of work, including extensive outcomes-linked tissue microarrays for immunohistochemical assessment of marker status and subsequent statistical analysis. However, the representation of some of the rarer tumour subtypes in these arrays is something we still need to work on.

At a meeting today, one of the stats guys handed the PI a group of Kaplan-Meier survival curves based on the expression of a candidate biomarker in different tumour subtypes. Some of the curves looked very promising indeed.

One of them looked like this:

The PI said, “you know, I’ve seen spin-off biotech companies formed in response to curves like this. Personally, I think I’ll hold off”.

I want to see a Kaplan-Meier curve showing bankruptcy-free survival of the companies using such data, compared to the companies using actual good data.

Remember these guys?

Eight of the nine survived – an excellent percentage, considering that Mum is a novice. I finally got to meet them this weekend, and uncharacteristically remembered to bring the new mini video camera my sister got me for Christmas. I’m still learning how to use it (and iMovie), so please bear with the terrible camera work!

Happiness is a room full of puppies… minus the smell! Oh, and also falling asleep curled up on a sofa with the puppies’ gigantic mother while all your friends party around you. In my defense, it was 2:30am after a night of pasta, wine, dancing to an eleven piece funk band (three drum kits and lots of brass), capped off with a starlit soak in a hot tub…

I have to admit that when I first moved to the BC Cancer Agency in 2002, I knew very little about it. I found my new lab through a strategic PubMed search rather than by browsing the BCCA website, and no-one else in my PhD lab showed any sign of recognition when I told them of my destination.

Things changed in 2003, when I started getting emails asking if my lab had been involved in the SARS genome sequencing project (no, but I had friends at the Agency’s Genome Sciences Centre who were on that paper). By the time I returned to the BCCA in 2007 after a two year stint in industry, my scientist friends in other countries had heard of my new boss, although a couple of them seemed surprised that he’d left Cambridge for the scientific backwaters of Vancouver.

In the last few months, though, my colleagues have published a series of papers that are bringing them much more recognition. The papers themselves are very high profile:

Shah et al: Mutation of FOXL2 in Granulosa-Cell Tumors of the Ovary. New England Journal of Medicine 2009: 360:2719-2729

Shah et al: Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009: 461:809-813

Morin et al: Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature Genetics
Published online: 17 January 2010 doi:10.1038/ng.518

and the Agency has also really stepped up its PR efforts. I work with some of the main players behind the three papers linked above (some much more closely than others) and have been involved in drafting press releases and backgrounders. I sat in on some of the press conferences, listened in on my boss being interviewed live on the radio, and have seen the Agency and associated Foundation broadcast the latest news through their own blog and on Twitter. The announcement of the second paper even briefly hit the top ten trending topics on Twitter, which was almost as cool as seeing my boss being interviewed on the local morning news, as the first item on the CBC’s The National news programme, and on the front cover of the Globe and Mail.

Over the last year, I’ve had many more emails from friends in other countries asking “hey, is that your lab?” I’ve seen hits to our website and student / postdoctoral applications go through the roof. I’ve heard anecdotally that researchers in Toronto and the UK are sitting up and taking notice – one researcher in our field is even alleged to have said (and I paraphrase this third-hand information) “how am I supposed to recruit molecular pathologists to my lab when everyone knows all the best ones are in Vancouver now?”

So, when I was asked the following question in an email from a friend and former labmate:

“And how is your work going? Still enjoying it? No secret longings after pipettes, transformations and DNA extractions? Or the privilege of staring down a microscope?”

I replied with

“No longings for pipettes or related paraphernalia yet! Almost five years now! I love being this close to some really cutting edge research, without actually having to do any of it myself…”

So, Heather, nice try… I will never again be as close as you are to that thrill of the big discovery, but I’m close enough to satisfy my scientific itch, and I still get to drink the champagne.

Oh, and the reflected glory is nice, too. I was just the proofreader for one of the three papers I linked to, but I’ve helped write grants for, and am the project manager on, some ongoing work that I am confident will merit more top tier papers, press releases, and all that hoopla.

Science: never a dull moment!

I am one of several people using a single account to manage our department’s local research ethics applications. I logged in to the account this morning to extract an archived consent form to send to a collaborator, and saw a new application at the top of the page that really caught my eye:

“[PI’s last name] breeding protocol”

After doing a massive double take, I just had to check the most pertinent detail: was the application listed under “Animal Care”, or “Human Ethics”?

Luckily, it was the former.

Now I have to find out who named the protocol so I can go and thank him or her for the laugh.

(It definitely wasn’t the PI, by the way! And no, I don’t work for Hwang Woo-Suk.)

I first came across the BBC’s Dragons’ Den on a work trip home a few years ago. I instantly loved it; I was working in marketing at the time, and I genuinely did learn a lot from the successful pitches. But, of course, the real fun comes from those awful, doomed pitches, and the complete lack of self awareness of some participants.

I was really happy when the CBC came up with its own version of Dragons’ Den the next year, and I watch or tape it every Wednesday night. I no longer pretend to gain any career-related benefits from the show, and treat it as pure entertainment.

But this week’s episode was a little more serious. See how the Dragons deal with a snake-oil salesmen claiming to have a miracle cure for cancer, arthritis, heartburn, and pretty much everything else under the sun:

I have to say I was impressed. If only all sources of product development funding were so hostile to the woo-meisters and people sucking money from desperate patients. It helps that Jim Treliving, the Dragon who kicked the guy out, is a former cop who presumably has little patience for fools and knaves.

You may have noticed that I haven’t posted for a while. I have a backlog of ideas for posts that are suitable for my other blog, but nothing that fits this one.

Following the example set by our esteemed leader, I mused on Twitter the other day, “I have no ideas for proper science blog posts on Nature Network right now. Shall I just say I’ve prorogued my blog?”

A friend put an end to that with his reply: “I think you can only do that if you’re avoiding specific science and are pretty sure it’ll go away by the time you resume.”

I was hoping to use last night’s Vancouver vs. Edmonton “Skeptics in the Pub” pub quiz for inspiration, but I am sad to report that Kyrsten and I were not exactly assets to our team. In fact, we came joint second-last in Vancouver, and (we think) behind everyone in Edmonton.

But! The Official Spectator Guide that arrived with my Olympic tickets on Monday came to my rescue!

Flicking through its pages, I read with approval that every event ticket includes free access to all public transport on the day of, and up to 4 am on the day after, the event. We were already planning to take the bus and SkyTrain to all our events (except the one that’s within walking distance), so that was a bonus.

But then it all started to get a bit odd.

First of all, speed skating spectators heading to the Richmond Oval are advised to “Dress appropriately. As you’ll be walking along the Fraser River on your way to the venue, waterproof clothing and comfortable footwear are recommended”. I don’t know what this says about the quality of riverside path and railing construction, but it’s worth noting that my husband left at 6 o’clock this morning to spend a week building wheelchair access ramps for some of the Whistler venues. The entire crew are movie set carpenters. I’ve reminded him that the ramps are not supposed to collapse, explode, or otherwise provide any spectacular and/or hilarious visual effects. I’ve at least established that they’re using real wood, rather than plywood, or Styrofoam painted to look like wood.

I then decided to see where all our seats are going to be. Snowboard cross: general admission (standing), right at the base of the run. Men’s hockey (Canada vs. Norway): lower bowl, 21 rows back, in a corner. Women’s hockey (Canada vs. Sweden): upper bowl, behind a goal, but in a smaller stadium. Curling: nice and central.

Curling?

Yes, curling.

I know next to nothing about curling, but a) it’s pretty damn cool to walk to the Olympic Games from your house, and b) it’s one of Great Britain’s only real chances at a medal. We’ll see both Canada and GB play in a preliminary round, but not against each other, so I can cheer for both teams!

But at least now I know more about curling than I did before. The Spectator Guide says: “Did you know curling stones weigh 19.1 kilograms? That’s almost the same weight as four Vancouver Island marmots”.

Fascinating.

So, I hereby propose two new SI units.

One curling stone (1 CST) = Four Vancouver Island Marmots (4 VIM)

or

1 Vancouver Island Marmot = 250 mCST

The great thing is that the curling stone is also a unit of time and volume. Apparently, there are ten ends per curling match. Each end comprises 16 stones. A game can take a total of three hours. Therefore one stone (1 CST: do keep up) = 1.125 minutes. Your average Canadian curling spectator (and many a participant, too, although probably not in the Olympics) gets through one pint every eighteen minutes. Therefore there are 16 CST per pint.

It follows that there are 64 Vancouver Island Marmots per pint of beer.

That doesn’t seem like much beer each, even for a marmot.

“I can haz more beer, please? Surely u don’t expect me 2 watch curling while sober?”