Archive for November, 2009


A high-risk, high-return investment

In Sample-naming algorithm on November 8, 2009 by gcbenison

A colleague of mine – like me, a protein scientist – recently remarked that he had “spent all week making protein that fits in a tube half the size of your pinky finger”.

It’s an accurate description- even today, with all of the tools available, it takes about one person-week of skilled labor to make a sample of pure protein starting from scratch.  The process involves a series of steps, each of which must succeed, otherwise at the end of the week instead of a pinky-sized sample of protein you will have exactly nothing to show for your efforts.

In this way bench work is different from anything else I do as a scientist – such as writing manuscripts, reading, or debugging code – where a couple of hours invested is almost certain to result in something tangible being accomplished.  Only in bench work do I need to make a large investment of time not knowing if or when it will pay off.  The return on time invested in protein purification can be very high, though, especially for a novel protein.  Every protein is different, and know-how in working with a particular one can be a lab’s competitive edge, providing a foundation for a successful research program lasting years.  Successful collaborations can be built entirely on a lab’s ability to produce a desired protein, which traces back to that time initially invested at the lab bench.

So given the possibility of high return, how can one manage the risk associated with bench work?  How can I ever summon the courage to start a new protein purification, knowing that I may be about to embark on a colossal waste of time?

The answer, for me, is this: “The protein is not the product; the process is the product.”  Even in the course of a failed protein purification, every step generates a wealth of information about how that protein behaves under certain conditions.  If you capture that valuable information,  so that your next attempt can be better, your time will not have been wasted.  If, on the other hand, you focus only on the end product and let potential lessons fade away,  you have wasted your time indeed.

So how can you capture the lessons you learn during a purification?  It is not enough just to believe in the idea – you need a method.  In an academic lab, we usually don’t have the budget or the formality to use a commercial LIMS system.  Instead we have something more ad-hoc, often no more than the guideline to “write things down in your lab notebook”.  That’s pretty vague, leaving a lot of lattitude for people to develop their own systems for keeping track of samples.  In coming posts, I’ll share my system, and why I chose it.