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!