The scientific method comes in many guises. During the past eighteen months in the lab, I have suffered from a severe lack of hypotheses. Or rather, I have been laboring under the umbrella of one very big, very broad hypothesis-with-a-capital-H:
Genes in the same pathway will often exhibit similar phenotypes after individual knockdown.
This idea may seem self-evident, but it comes with a corollary that turns out to have much more potential:
A novel gene that, when knocked down, gives a similar cell morphological phenotype to that caused by knocking down individual members of a known pathway, might play a role in that same pathway – especially if these changes are conserved in disparate species.
In other words, genes that lead to the same conserved biological end result will manifest similar effects when removed from the system, and unknown genes can often be placed into known functional modules by associating their phenotypes with those of known functional clusters. It’s a fine guiding hypothesis, but it doesn’t lend itself to yes/no testing in the way that I’ve been used to thinking about the scientific method. At least not on the day-to-day timescale.
So it is when you embark on a large, high-content genetic screen. You study hundreds of genes, instead of just one, and hope that something interesting comes out. Mine is nowhere near as big as many large-scale endeavors: whole genome sequencing efforts, for example, or Craig Venter’s sea microbe project. But I must confess that in many ways, it has probably been as tedious. As all my colleagues assemble pieces of their one-gene or one-pathway puzzles, lovingly filling in what scientists like to refer to as their ‘story’, I annotate images and compile statistics. If something looks intriguing, I have to force myself not to follow it up lest I get lost in a thousand wild goose chases. I remember studying the image of a particularly striking image of a cell on my screen, and a fellow post-doc asking me what gene I’d knocked down to produce it. When I told her it was yet another gene of no known function, she asked me what it looked like, what sort of domains the protein contained. When I told her I hadn’t even looked at the sequence, she was shocked. But there isn’t time: this is strictly big picture. You have to stifle your natural curiosity in the name of getting things done. It’s like having to make all your own toys, line them up on a shelf and inventory them before you’re allowed to play with a single one.
But finally, playtime is about to begin. Having finished my inventory and done a few validations, I’ve discovered an extremely interesting gene. When you knock it down in human cells, or its homologue in fly cells, the morphological changes that result are the spitting image of something very familiar indeed. And when you look up what this novel gene is, you realize immediately that there is something about what little we know of its structure and function that makes perfect sense as far as linking it in with this more familiar pathway. As all gene discoverers realize, it’s far more fun to work on a gene about which a little is known than to start from square one on a completely blank slate. Otherwise, it’s like embarking on a treasure hunt without the first paper clue in your hand.
And so it was that on Wednesday, my last day in the lab before the Christmas break, I was able to write my first real, day-to-day, hypothesis-with-a-small-h in my notebook:
It was, I admit, hard to leave work with this tantalizing blank waiting to be filled, but it will still be there, patient and unresolved, on my return in January. If there is one thing I have learned in my years in the lab, it is that the story is never finished – so you might as well enjoy your holidays.
Happy Christmas all!
Ooh! Ooh! I can’t wait! Get back to the lab! I want to know what it is and what it does!
My bench is free until 5 January if you want to have a go!
Right, I’ll be there!
As usual, Jennifer, you’ve described it to a T:
“And when you look up what this novel gene is, you realize immediately that there is something about what little we know of its structure and function that makes perfect sense as far as linking it in with this more familiar pathway. As all gene discoverers realize, it’s far more fun to work on a gene about which a little is known than to start from square one on a completely blank slate.”
Have a delightful vacation and enjoy the antici…pation.
Ha! Heather, I love that song. In graduate school, I even used one of its couplets as an (only slightly) ironic, semi-drunken chat-up line:
_Why don’t you come up to the lab
and see what’s on the…slab?_
Did it work?
For those not in the know, Richard was a cultural anthropologist specialized in lab-related chat-up lines in his previous incarnation.
Sounds dangerous. I’m not messing with him.
But wouldn’t it be great if someone cited his chat-up lines in a peer-reviewed journal?
None of those worked, either.
How did we get from hypotheses to chat-up lines?
(Oh, yes, that’s right. Never mind.)
Just as an update, after four days off, the imperative of that shiny new result is already starting to fade and become abstract. It’s amazing how thoroughly real life can take over if you allow it. (Is it like vampires? Do you have to invite it in?)
Jenny, how exciting! When you close your eyes, I bet you have little genes (or microarrays, or motifs, or whatever), dancing before your inner eye. I bet you see them in every puddle and cloud, in every innocent drift of leaves on the sidewalk. I know that feeling too – one of the finest sensations you can have with your clothes on, an epiphany almost as thrilling as playing a Hammond in a crowded bar … oooh …. I’ll have to lie down, now.
Interestingly, I do tend to see my cells everywhere, especially after a long day of staring at them, but it’s strongest in the toilets. Something about the patterns on many bathroom floors calls up the appearance of a formerly healthy monolayer ravaged by some grotty phenotype or another. It’s positively mesmerizing.
When I spend loads of time at the microscope, as when I’ve screened hybridomas or cranked out neuron survival data, I can’t stop seeing the cells. This can become so pervasive that it influences my artwork, which is often surreal enough without the intrusion of laboratory items (and which is meant to be relaxing).
As a postdoc, in the midst of finishing survival assays for a manuscript, and beginning to characterize a mouse cancer model, I worked on a colored pencil piece that featured giant mice and neurons taking over the city skyline, which I could see out the lab window. The mice and neurons were taking over my life, so why not the city as well?
Can you post an example? I’d love to see…
Jenny, the cityscape with mice and neurons was relinquished in a bet that I lost (I didn’t think the manuscript in question would be accepted by a shiny glamour journal, and it was), so I no longer have access to it.
My artwork nowadays is usually more environment- than lab-influenced, but I need to scan or photograph some of it for submission to our university art and creative writing journal, in electronic format. I can post some of the images here, in my blog. I’ll also bring my art journal/sketchbook to CISB09, so that anyone can peruse it if they like (most of it is nature-themed).
You can also submit some to LabLit. We love science-y geeky art.
You’ve all seen my koala, haven’t you?
Doesn’t look much like a koala … [squints, looks closer] … a yes, I see what you mean. However, if you hadn’t’ve told me, I’d have thought it looked more like a satellite picture, had satellites been invented, of the main positions of the army of Scipio Africanus just before the Battle of Zama in 2002 BC, the decisive victory over Carthage. A back view, obviously.
Just what are they putting in the drinking water in Cromer, Henry?
Hey, buster, it’s you that’s posting these weird pictures, not me. I’m just telling it like it is.
I’ll also bring my art journal/sketchbook to CISB09
I am trembling with ant-i-ci-pa-tion!
I am trembling with ant-i-ci-pa-tion!
Oh, dear, I’m afraid most of the journal is pretty mundane, such as sketches of plants and birds in my yard, or things that I find on walks. Like this:
I might be slightly obsessed with echinoderms.
The Gees Minor and Minima would love this, also being obsessed with echinoderms – the fossils we find, now and then, on Cromer beach, are Cretaceous echinoids weathered from the chalk bedrock.
Kristi, those are heartbreakingly beautiful sketches. Thanks for sharing.
p.s. where did you put the full moon after you found it on your walk?
The moon? Why, I threw a lasso around it and pulled it down. Easy! 😉
I know a couple of rural-residing scientists who keep farm journals, and write details about temperature, moon phases, rainfall amounts, seeds planted, harvests, etc. I suppose I was doing a bit of that, though I live in suburbia.
Jenny> I’d be happy if the hypothesis was correct after a few more experiments and more thoughts…. the last one was a tad bit “altered” when I found my new bacterial results.
Ah well, it is nice once you form one for “real” though. And it will be fun to hear more about your phenotype and what really goes on there.
Yes, Asa, that’s the problem with following up hypotheses instead of basking in them. The high probability that it will all come to nothing!
Don’t grow too attached to your hypotheses.
I think I’m in love with the drawing of the red seed pod, Kristi.
@ Richard – The seed pod was sketched using my preferred medium, colored pencil. The best colored pencils, IMO, are made by Prismacolor, and I took a class a number of years ago, for which we were encouraged to buy the set of 120 different colors. I need to replace Black Grape and Indigo Blue very soon, because I use them for shadows all the time.
I love Prismacolors! I always wore the green ones thin.
What is it about pencils and geeks? I have a pack of pencils in my drawer right now (how did the HBs get in with the #2s?) and the pack of crayola coloured pencils I bought so that I could solve my first NMR structure. >sniff
Did you have to do it between recess and gym class?
I seem to remember doing it on the living room floor and trying to stop Rachel from chewing the pencils.
I once left a school shopping list for my Mum including “blendable pencils”. She misread my writing and greatly amused the WH Smiths’ sales assistant by asking where the “bendable pencils” were.