Tuesday, March 29, 2016

The Climb

I’ve been working as a simulation biologist for over year now, so I’ve gotten pretty used to instant (or nearly instant, depending on how sloppy my coding is) gratification. A few hundred lines of Python, a handful of bug fixes, and a few minutes of code-running on my speedy work computer, and

I’ve simulated 10,000 tumors treated with 10,000 different cancer drugs for 100 days each. Here they are, all plotted on this trippy heatmap.

Pretty sweet, huh? Were I a wet-lab oncologist performing the same experiment, I could grow and treat, say, twenty rat tumors at a time. That’s twenty tumors for every 100 days. So… The tumor growth and treatment alone would take 50,000 days, which is a mere 137 years. And presumably it would take me a second or two to engineer those 10,000 drugs with very specific uptake and degradation parameters.
But hey, you know, sometimes you want to stop and smell the Petri dishes. I think wet-lab biology is about the delayed gratification—as Miley Cyrus would say, it’s about “the climb.”

Well, figuratively.

Wet-lab work has its advantages. I don’t have to make up any numbers, the road to publication is less treacherous, the intellectual leaps are smaller, and things are more certain in general. 

And often the math is much less onerous.

So here I am in 20.109, smelling the Petri dishes.

Well, not so much. We started out in silico, designing a pRSET plasmid we could cleave up to insert the gene for our protein of interest, a calcium sensor. We’d embarked on our quest to build a better calcium sensor—or at least a more sensitive one.

Not even on day two could I abandon my computer: next was designing primers for site-driected mutagenesis. I guess wet-lab work isn’t all dish-sniffing, after all.

But then it began: Oh, the pipetting! The gel electrophoresis! The algebra, the inscrutable buffer acronyms, the aspirator backwash, the gloves, the lab coats!

… And the mistakes. The “Oh, we need four milliliters of solution mix? We made four microliters…” The ruptured growth media, the indecipherable gel runs, and the poorly-balanced centrifuge nearly hopping off the table.

And so it continued, on and on for another three weeks of protein expression in real live E.coli (!),  mini-preps, protein purification, pipetting, and calcium titration.

Along the way, we got a few bits of data about how our designer protein was doing. We confirmed uptake of IPC into the pRSET plasmid. We sequenced our mutant plasmid—our mutagenesis worked! Our E.coli took up the plasmid, and the wild-type IPC sensor worked beautifully.

Everything was going great, and the suspense was really killing me.  Would our new IPC out-sense the original? Would it be better suited for the cytosolic environment?  Could it cure cancer?

And thus our great hopes hinged upon the outcome of the Ca2+ titration assay. The reader whizzed, buzzing past each well in the plate, recording fluorescence measurements. We rushed back to our laptops and entered our data, plotting the graphs that would determine our protein’s fate!

And, well, we got a line that was pretty darn flat. Our protein was totally indifferent to the presence of calcium. Remarkably insensitive—and entirely useless, to be frank.

And so I learned: bench biology isn’t about the delayed gratification—it’s about the patience.

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