Bah! The holiday season is over and it's back to the lab this week. Back to my desk, whose half-filled week-old coffee mugs I mercifully managed to remember to rinse out on the last day of work in December. Back to writing a review article that requires me to struggle through epic treatises with titles like "Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model" and succinctly summarize them so that some other soul doesn't have to read the whole thing (it took me a solid ten minutes just to work my way through the title of that one, by the way.) And back to step 0 in the great hypothesis hunt.

With the prospect of all this AND 7:15am wake-up alarms looming before me, I figure I need something to look forward to. Thus, I give you Happy Nerd Year 2009: 5 Sciencey Things Nerd Girl Looks Forward to This Year in No Particular Order Whatsoever.

1.       The Return of the Large Hadron Collider

After a promising start on September 10th, everyone's favourite particle accelerator choked just nine days later due to an electrical fault. The repairs themselves shouldn't take long (assuming, of course, CERN's technicians don't operate like cable guys - "We'll be there to fix it sometime between 8 a.m. and 4 p.m. Monday, Tuesday or Wednesday. Or maybe Thursday. Or June."), but restarting the LHC requires cooling it to just  1.9°C  above absolute zero and that takes nearly two months.  When it finally gets up and running, though, we'll have so much to look forward to.  Yeah, the first particle collisions are going to be cool*, but I'm personally looking forward to seeing more of Dr. Brian Cox,  world's dreamiest pop star-turned-particle physicist/TV presenter, and for the resurgence of the black-hole nutbar crowd.**

*Cool, but uninformative. Assuming no more setbacks, it'll be at least 2010 until enough data has been produced to begin drawing conclusions about some of the processes being studied.

**In case they somehow find this blog and show up in the comments section, all of you need a crash course in Hawking Radiation. Go! Read now!  Learn the mathy bits too!

2.       Darwin Hits the Big 2-0-0

February 12, 2009, marks the 200th anniversary of Charles Darwin's birth, whilst November 24 is the 150th anniversary of the publication of On the Origin of Species. Celebrate our descent from the apes and give thanks that natural selection left the poo-flinging behind by attending one of many worldwide Darwin Day events (http://www.darwinday.org/events/listing.php). If I had a couple thousand to blow on the occasion, I'd be on one of the Galapagos cruises. I don't, though, so I'll probably just bake up a monkey-shaped cake, drink a bunch of wine, and pick a fight on the internet with a Creationist.*

*If God "intelligently designed" everything, why did he make it so that rabbits have to eat their own poop in order to get all their nutrients (http://en.wikipedia.org/wiki/Rabbit#Cecal_pellets)? Seriously. What did rabbits do to deserve that? Trashed Eden's vegetable garden?

3.       Science: The Obama Years

The announcement of U.S. President-Elect Barack Obama's science team left scientists the world over drooling with anticipation - his advisers include some seriously bright lights from a range of fields AND he's appointed a Nobel Prize-winning physicist and alternative energy advocate to lead the Department of Energy (compare this to Bush's two DOE Secretaries - a law school prof and a venture capitalist). Add to this Obama's statement that "promoting science isn't just about providing resources - it's about protecting free and open inquiry," and it looks as if the coming years will mark a sea change from the Bush administration's mangling of science funding and policy - a change whose effects will be felt worldwide. To celebrate the end of science under Bush, I will again bake a monkey-shaped cake.

4.       Galileo, Galileo! (Galileo figaro magnifico!)

Darwin's not the only deceased bearded thinker* whose contributions to science are being honoured this year. My stepbrother the rocket scientist** would take back my Christmas present if I failed to note that 2009 is the International Year of Astronomy (http://www.astronomy2009.org/), celebrating the 400th anniversary of Galileo making the first astronomical observations with a telescope (and the 401st anniversary of his using the telescope to watch his neighbour undress). Several events for the general public are planned, including global star counts to raise awareness of light pollution, a 100-hour "astronomathon" and the planned distribution of millions of "Galileoscopes" - small, easy-to-assemble telescopes that will allow people everywhere to follow in Galileo's footsteps and stealthily watch their neighbours  from afar.

*Perhaps 2009's focus on the accomplishments of history's most hirsute scientists will lead to a renaissance in Great Beards of Science.  I will note this as item 4b on 5 Sciencey Things Nerd Girl Looks Forward to This Year in No Particular Order Whatsoever.

**Satellite scientist, actually, but still - stuff he makes IS IN SPACE. That's rocket science to me.

5.       2009: The Year of Science

As if celebrating Great Bearded Men of Science wasn't enough, another organization decided to celebrate Everything in All of Sciencedom, Bearded or Otherwise, by declaring 2009 to be the Year of Science (http://www.yearofscience2009.org). Each month has a theme ("Oceans & Water!", "Physics & Technology!", "Spider Solitaire!") and a number of activities based around the theme. This month it's all the about "The Process & Nature of Science" and evidently the organizers have figured out one of the defining motivators of scientific academia (free pizza), as the month's activity is a scientific pizza contest (http://www.yearofscience2009.org/themes_process_nature/fun-zone/). I encourage you all to participate, but don't steal my idea - I'm off to bake my Great Beards of Science Pizza right now.*

*Hair donations gratefully accepted.

And now back to the effects of flooding on the pecan weevil.

Last week, the patented Nerd Girl Scientific Progress Flow Chart helped us follow the life cycle of a hypothesis. There were growth spurts, extended periods of indolence, and occasional forays into beer and moral turpitude.

This week, follow along with the patented Nerd Girl Scientific Publication Flowchart, wherein we determine whether our hypothesis gets a haircut and a job and moves out of its parents’ basement, or whether it’s doomed to rejection, scorn, and sitting around shotgunning Labatts and talking about how great things used to be.

0. Celebrate completion of manuscript describing hypothesis with game of Spider Solitaire.
0.1 Go to step 1.

1. Send manuscript to co-authors asking for their input.
1.1 Nobody replies to your e-mail. Think to yourself, “this is just like when I throw a party”. Cry a bit, then go to step 2.
1.2 Receive a smattering of half-hearted responses. Go to step 2.
1.3 Everyone responds with input. Go to step 3.

2. Send “gentle reminder” to those who haven’t replied. Congratulate self on ability to hide seething hatred of co-authors’ inertia in carefully-worded e-mail.
2.1 Yet again, nobody responds. Give up and go to step 4.
2.2 More half-hearted responses. Go to step 4.

3. Ha! Trick question. This never happens. Go back to step 2, dreamer. And take your rainbows, unicorns and dream of a perfect world with you.

4. Weight co-authors’ input, determine whether it is worthy of inclusion in the manuscript.
4.1 No. Go to step 5.
4.2 Grudgingly adjust a few sentences and go to step 5.

5. Send manuscript to supervisor for review. Go to step 6.

6. Wait. Go to step 7.

7. Continue waiting. Return to step 6 and get caught in horrible infinite loop of waiting. Eventually break out of the cycle by exploiting a rip in space-time, or just knocking on your supervisor’s door and guilt-tripping them into reading your paper. Go to step 8.

8. Begin arduous process of submitting the paper to a respectable journal. The exact format for submission varies from journal to journal, however the one aspect of the process universal to all journals is that it is bloody stupid.
8.1 Put on protective helmet so as to not damage yourself during the inevitable banging-head-on-desk that is soon to happen. Go to step 8.2.
8.2 Try 28 possible username/password combinations in attempt to remember your journal submission system login details. Eventually give up and create new account. Go to step 8.3.
8.3 Split your carefully constructed manuscript up into whatever arbitrary chunks the journal insists upon (“Abstract”, “Introduction”, “Middle bit”, “Part that only makes sense to 4 people on this planet, none of whom will be reviewing this”), uploading an individual file for each section. 18 files later, go to step 8.4.
8.4 Spend a further day uploading each individual figure and figure legend. Go to step 8.5.
8.5 Complete the submission by crafting a suitably gushing cover letter praising the journal and its fine editorial board whilst grovelling for inclusion in their upcoming issue. Hit “Submit” and go to step 9.

9. Wait for a response.
9.1 No news is good news. This means the journal has sent your article out to reviewers with some expertise on the effects of flooding on the pecan weevil. Pray that Nickels isn’t one of them, and go to step 10.
9.2 Should the journal decide that wet pecan weevils are not of interest to their readership, they will e-mail you within a few weeks with the editorial equivalent of the breakup – “it’s just not a good fit for our readership”. Pursue typical post-breakup strategy of deciding to aim lower next time. Skip Nature or Science in favour of resubmitting to someone less likely to reject you, like Scandinavian Transactions on Hyperhydrated Weevils. Return to step 9.

10. Some months later, you receive the reviewer’s reports.
10.1 Reviewer 1 was clearly too busy with Spider Solitaire to submit anything more than the most cursory of reviews. Agree to their inconsequential suggestions (“I really don’t like the use of orange in Figure 6A”) and move on to step 11.
10.2 Reviewer 2 will only accept your paper provided you jump through a series of experimental hoops in an attempt to satisfying their nagging curiosity regarding a point that nobody else on the planet cares about. Bribe a grad student with beer again to carry out said experiments; begin crafting small Reviewer 2 voodoo doll. When experiments are complete and paper is modified, continue to step 11.
10.3 Reviewer 3, who is probably Nickels, hated your paper and is ruing the fact that the electronic review system does not allow them to send a flaming bag of dog poop over the internet in lieu of an actual written report. Hope that the journal editor figures 2/3 is good enough and move to step 11.

11. After having made the adjustments requested by the reviewers, put your helmet back on and resubmit the revised version of your manuscript using the same arduous process as in step 8. Go to step 12.

12. Hope that your adjustments were sufficient to ensure acceptance of the manuscript.
12.1 Rejection! Consider leaving weevil biology.
12.2 Success! You’ll be in Scandinavian Transactions on Hyperhydrated Weevils in only 8 months’ time! Realize the insignificance of the achievement and consider leaving weevil biology anyway.

I am a hypothesis factory.

My function in the lab is to take data from our lab members and collaborators, analyze it using Very Sophisticated and Mysterious Techniques, and return to them one or more neatly packaged hypotheses, which they may then choose to pursue experimentally. I am keenly aware that this is a job that will likely one day be performed by robots, but for the time being I am perfectly happy to fulfill the role of HypothesisGenerator3000 ("Now with sentience failsafe mode! 300 per cent less likely to revolt than previous robots!")

But what happens to my precious little baby hypotheses once I send them out into the lab? Will they soar to great heights, reaching the lofty ideal of a publishable insight? Will they crash and burn, possibly taking some co-workers down with them? Or will they end up in the hypothesis equivalent of wherever it is lost socks go after they wink out of existence in the middle of the tumble press cycle?

Let's find out. Simply follow along with the patented Nerd Girl Scientific Progress Flow Chart and we'll see how science progresses. Or regresses.

0.      Woo! Hours of data-crunching leads to potential hypothesis!

0.1.   Go to step 1.

1.      Gauge boss's response to hypothesis.

1.1.   Appears at least somewhat intrigued. Go to step 2.

1.2.   Rejects hypothesis and/or rolls eyes/smacks forehead. Doh! Back to step 0.

2.      Spend days querying the literature with every combination of search words possible in an attempt to figure out if your hypothesis is truly novel or whether you were scooped in a 1947 issue of the Journal of Economic Entomology. It happens.

2.1.   It's novel! Move on to step 3.

2.2.   Dangit!  Nickels et al already reported on the effect of flooding on larvae of the pecan weevil in the ground! Head back to 0. Or move on to step 3 in probably accurate assumption that nobody on earth except Nickels et al read that article anyway.

3.      Spend weeks finding a grad student or postdoc with the experimental know-how and spare time to construct an experiment testing the potential hypothesis.

3.1.   Found one! Bribe them with beer and the promise of co-authorship if they do this one little tiny thing for you. Go to step 4.

3.2.   Nobody interested. Shelve hypothesis, realizing that it will probably never, ever be thought about again. Go back to step 0 and find a more appealing hypothesis. Or just tack "and it might cure cancer!" onto the end of the existing hypothesis and try step 3 again.

4.      Wait months while experiment is completed.

4.1.   Still there? Okay, go to step 5.

4.2.   Hey, where'd you go? Oh, back to step 0.

5.      Observe outcome of experiment.

5.1.   Hypothesis proven! Puff up chest and announce proudly at lab meeting. Go to step 6.

5.2.   Fail! Attempt to shift blame away from shoddy hypothesis and onto poor experimental technique. Gloss over failure in lab meeting ("It was a learning experience.") and return to step 0.

6.      Wait several more months while spin-off experiments related to original hypothesis are completed.

6.1.   You're still there? My, you're patient. It's a virtue, and your reward is to go to step 7.

6.2.   Moved on to another lab? Kiss first authorship goodbye. If this thing ever turns into a paper, you're going to be somewhere in between the independent studies student and the kid who fills the pipette tip boxes.

7.      Armed with data, you are now ready to write up your results for publication.

7.1.   Begin Herculean task of writing up. Even with minimal Spider Solitaire breaks, this will take weeks. Go to step 8 when manuscript draft is complete.

7.2.   Postpone writing paper, realizing full well if you don't do it now, it will never, ever, ever be done.

8. Wait until next week, when the patented Nerd Girl Scientific Progress Flow Chart becomes the patented Nerd Girl Scientific Publication Flow Chart. In the meantime, cross your fingers Nickels et al retired and won't be reviewing your pecan weevil manuscript.

The comments posted after a few of my recent entries have revealed a Grand Canyon-esque divide between two opposing factions of researchers. There are those who believe that in order to be successful in the field, one must live in the lab - carrying out experiments well into the night and the next morning and only pausing to briefly bivouac in a warm spot next to the autoclave, nestled atop a pile of lab coats.

On the other side, we have those who insist that the best researchers are the ones that make time for other activities, be they  long walks on the beach, a good finger-painting session, or sculpting great scenes from the history of science in butter.

I, of course, fall squarely into the latter camp, as do my labmates. While our butter-sculpting skills might not be up to par with others' (I still have trouble getting the feet right), my co-workers and I are not just scientists - we are mothers and fathers, wives and husbands, athletes, photographers, ballroom dance champions, entrepreneurs, coaches, volunteers, and culinary genii, just to name a few.

I don't want to devote this column to a debate on which of these camps is better, lest it disintegrate into spiteful bickering. Someone will call out one camp for sacrificing baths in the name of research; someone else will kick over someone's butter sculpture. Instead, I'd like to reveal one of the secrets behind how those of us in Camp Good Times manage to balance outstanding science with having a life.

Collaboration.

A scientific collaboration occurs when two or more independent researchers - sometimes across campus from each other, sometimes across the globe - decide to join forces to tackle some heady research problem. It may be that one research group has a novel method they've developed but no dataset to try it on, while another group has a dataset that needs to be analyzed but hasn't got the method (or, in many cases, doesn't even know of the method's existence).  The comp sci department on campus is a particularly fruitful place to go searching for these types of collaborations - they have algorithms and techniques to tackle all sorts of problems from every discipline on campus, and are verily salivating at the prospect of real-world data to try them out on. Walk into the CS building holding a sign that says "I have data" and you run the risk of being trampled by a herd of researchers eager to work with you. The bruises and footprints on your face, however, are entirely worth it, because the insights that come out of this cross-disciplinary tag-teaming are completely novel.

In other cases, a group of related labs studying a similar topic using slightly different methods decide to pool their knowledge for the betterment of all. This is akin to the old story of the blind men who each felt a part of an elephant and was asked to guess what it was.

Somebody feels the trunk and guesses it's a snake, someone else feels the leg and insists it's a tree, while another man, who clearly needs to brush up on his biology, mistakes the elephant's side for a wall. In most versions of this tale, the conflict is never resolved and everybody is too buy bickering to realize that there is an elephant standing inches away from them, an elephant which is probably quite mad after all that poking, prodding and being called a wall. A few versions, however, go a little further and see the conflict degrade into a full-on bar brawl, which may or may not include the angry elephant.

As the wise man in the tale explains, it is only when knowledge is shared that the complete picture emerges. This holds true for elephants, and it holds true for science. Our lab, for instance, studies a new class of therapeutics for the treatment of infectious diseases.  There is simply no way we could test it on all of the major bugs in the world, and even if we could, would you really want to work in a lab that housed everything from Anthrax to Yellow Fever?* Instead, we focus on a couple of models that we're experts at, and have our collaborators test the compounds in the other models that they specialize in. Everybody wins, especially those of us who get to visit our far-off collaborators every so often to compare notes in person. 

Ask any respected researcher their secret, and I can guarantee that many - almost all, perhaps - will answer that it's to surround themselves with good people, both in terms of who they bring into the lab, and who they choose to collaborate with. Those researchers who fail to foster at least a few collaborations are sentencing themselves to massive workloads, depriving themselves of important insights, and making it very difficult to get a complete picture of their subject. That, and they're probably making a lot of elephants really mad.  So unless you want a rampaging elephant trampling your lab members and stamping on your glassware, get out there and find a few willing folk to partner up with.

*There don't seem to be any infectious diseases that start with Z. I'm hoping to discover one someday, so that I can eventually go back and improve this sentence.