Tuesday, 20 May 2014

Trivial or black-boxing?

I noticed today that I have a particularly unhelpful habit. It might have contributed to hundreds of hours of my time, and I feel they could have been saved with a simple question:

"Is this trivial, or should I black-box it?"

Let me explain.

As part of learning new skills, I will often come across things I don't understand. At this point, I am reaching the limits of my own knowledge and need some assistance in stretching that further to encompass something new. For example, at the moment I am learning how to take data for patch-clamp recordings and use these to estimate parameters for ion channel gating mechanisms using the Hodgkin-Huxley formalism. What I have had difficulty understanding, was how certain protocols were appropriate for parameter estimation. I have sought out further knowledge (patch-clamp recording protocols), consolidated past knowledge (gating mechanisms in Hodgkin-Huxley formalism), and for the most part all is well.

A lot of time could have been saved if I had appropriately interpreted the message my supervisor had given me. She said

"You just fit it"

I interpreted this to mean that it was a trivial exercise. That I should be able to work it out in a back of the envelope style way, or with a simple algorithm. Instead, I should really have interpreted as a black-box. It was not trivial, but I don't really need to concern myself with the details. In this case, once you have the equations, you feed it through a (mostly*) black-boxed optimisation algorithm and run your data through until you get a good fit. It seems obvious in hindsight.

However, my personal tendency is to believe that I must be doing something wrong, or that everyone else finds it easy and therefore I must be an idiot for not getting it. My personal coping mechanisms for dealing with my own ignorance.

This is what I could avoid with that simple question. When something is presented in such a way that it is mostly skimmed over, it could either be trivial or black-boxed. So I should just ask, and save myself the hassle.

* I actually quite like looking over optimisation algorithms. Even while I was wasting time looking up things that didn't help me at all, I was half concocting some Bayesian method for investigating whether there were differences in the uncertainty of parameters for persistent and transient currents with the standard protocols used for collecting these kinds of data.

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